Ok i finally got this to work the way i want it to. Thanks to Francesco for making me go down the ViewModel route. Ill post the entire code (there is a lot)

@model ZITS_BO.ViewModels.vmEquipment

@{
    ViewBag.Title = "Create";
    ZITS_BO.boEquipment be =new ZITS_BO.boEquipment();
    ZITS_BO.boCustomProperties bcp = new ZITS_BO.boCustomProperties();
   
}

<div  class="equipmentHeader">New Equipment</div><br />

 <script type="text/javascript" src="../../scripts/jquery.fancybox.pack.js"></script>
  
        
    <script type="text/javascript">
   
           $(document).ready(function () {
            $(".fancyboxEquip").fancybox({
                'type': 'iframe',
                'height': 400,
                'width': 800,
                'maxWidth': 800,
                'maxHeight': 400,
                'beforeShow': function () {
                    $('iframe').contents().html('Hello');
                    
                },
                'beforeClose': function () {
                    var sender = this.element.attributes[0].nodeValue;
                    sender = sender.substring((sender.indexOf("/") + 1), sender.lastIndexOf("/"));
                    $.post("/Equipment/reloadEquipmentType", { ssender: sender }, function (data) {
                        $('div#' + sender + '.data').html(data + '<a class="fancyboxEquip" href="../'+ sender + '/Create"><img title="Click here to add Equipment Type" class="equipmentAddImage" src="../../Content/Images/add-icon.png" alt="Add" /></a>');
                      
                    })

                }
            });
        });
        $(document).ready(function () {
            $(".fancybox").fancybox({
                'type': 'iframe',
                'height': 400,
                'width': 800,
                'maxWidth': 800,
                'maxHeight': 400
            });
        });

        $("a.ancybox").each(function () {
            var tthis = this;
            $(this).fancybox({
                type: 'iframe',
                'height': 800,
                'width': 800
            });
        });
        function checkSerialExists() {
           
            $.post("/Equipment/checkSerialExists",
            { serialNumber: $("#serialNumber").val() },
                function (data) {
                    var myObject = eval('(' + data + ')');
                    var newid = myObject;
                    if (newid == 0) {
                        $("#serialNumberDiv").html("");
                    }
                    else {
                        $("#serialNumberDiv").html("<font color='green'>This Serial Number already exists. Click <a class='ancybox' href='../equipment/serialSearchIndex/" + $("#serialNumber").val() + "' target='_blank'>here </a> to view the entry </font>");
                    }
                });
            }

            function showCustomProperties() {
                $.post("../CustomPropertyNames/loadProperties",
                    { equipmentType_id: $("#lstEquipmentType").val() },
                        function (data) {
                            $("#customProp").html(data);
                        });
            }


            $(document).ready(function () {
               
                if ($("#lstEquipmentType").val() != "") {
                    showCustomProperties()
                }
            });
                    
            

</script>





@using (Html.BeginForm())
{

    @Html.ValidationSummary(true)
  
    <fieldset>
   
       <table>
       <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.EquipmentType_ID, "Type of Equipment")
        </td>
        <td class="editor-field">
       <div id="EquipmentType" class="data">
            @Html.DropDownListFor(model => model.equipData.EquipmentType_ID, null, "Please select a value", new { @class = "dropDownStyle", id = "lstEquipmentType", @onchange = "showCustomProperties()" }) <a class="fancyboxEquip" href="../EquipmentType/Create"><img title="Click here to add Equipment Type" class="equipmentAddImage" src="../../Content/Images/add-icon.png" alt="Add" /></a>
            @Html.ValidationMessageFor(model => model.equipData.EquipmentType_ID, null, new { @class = "ui-state-error" })
        </div>
        </td>
    </tr>
    <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.SerialNumber, "Serial Number", null)
        </td>
        <td class="editor-field">
            @Html.TextBoxFor(model => model.equipData.SerialNumber, null, new { @id = "serialNumber", onblur = "checkSerialExists()" }) <div style="display:inline;" id="serialNumberDiv"></div>
            @Html.ValidationMessageFor(model => model.equipData.SerialNumber)
        </td>
    </tr>
    <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.Manufacturer_ID, "Manufacturer")
        </td>
        <td class="editor-field">
         <div id="Manufacturer" class="data">
            @Html.DropDownListFor(model => model.equipData.Manufacturer_ID, null, "Please select a value", new { @class = "dropDownStyle" }) <a class="fancyboxEquip" href="../Manufacturer/Create"><img title="Click here to add Manufacturer"  class="equipmentAddImage" src="../../Content/Images/add-icon.png" alt="Add" /></a></div>
            @Html.ValidationMessageFor(model => model.equipData.Manufacturer_ID, null, new { @class = "ui-state-error" })
            
        </td>
        </tr>
        <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.Model)
        </td>
        <td class="editor-field">
            @Html.EditorFor(model => model.equipData.Model)
            @Html.ValidationMessageFor(model => model.equipData.Model)
        </td>
        </tr>
        <tr>
         <td class="editor-label">
            @Html.LabelFor(model => model.equipData.BusinessUnit_ID, "Business Unit")
        </td>
        <td class="editor-field">
         <div id="BusinessUnit" class="data">
            @Html.DropDownListFor(model => model.equipData.BusinessUnit_ID, null, "Please select a value", new { @class = "dropDownStyle" }) <a class="fancyboxEquip" href="../BusinessUnit/Create"><img title="Click here to add Business unit" class="equipmentAddImage" src="../../Content/Images/add-icon.png" alt="Add" /></a>
            </div>
            @Html.ValidationMessageFor(model => model.equipData.BusinessUnit_ID, null, new { @class = "ui-state-error" })
        </td>
        </tr><tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.Location_ID, "Item Location")
        </td>
        <td class="editor-field">
         <div id="Location" class="data">
            @Html.DropDownListFor(model => model.equipData.Location_ID, null, "Please select a value", new { @class = "dropDownStyle" }) <a class="fancyboxEquip" href="../Location/Create"><img title="Click here to add Location" class="equipmentAddImage" src="../../Content/Images/add-icon.png" alt="Add" /></a>
            </div>
            @Html.ValidationMessageFor(model => model.equipData.Location_ID, null, new { @class = "ui-state-error" })
        </td>
        </tr><tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.Warranty, "Warranty Length")
        </td>
        <td class="editor-field">
            @Html.EditorFor(model => model.equipData.Warranty)
            @Html.ValidationMessageFor(model => model.equipData.Warranty)
        </td>
        </tr>
        <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.Value, "Value of Equipment")
        </td>
        <td class="editor-field">
            @Html.EditorFor(model => model.equipData.Value)
            @Html.ValidationMessageFor(model => model.equipData.Value)
        </td>
        </tr>
        <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.OrderDate, "Date Ordered")
        </td>
        <td class="editor-field">
            @Html.TextBoxFor(model => model.equipData.OrderDate, null, new { @readonly = "readonly" })</td>
            <td class="ui-datepicker"> @Html.Partial("_DatePicker", null)
            @Html.ValidationMessageFor(model => model.equipData.OrderDate)
        </td>
        </tr>
        <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.StartupDate, "Date equipment first used")
        </td>
        <td class="editor-field">
            @Html.TextBoxFor(model => model.equipData.StartupDate, null, new { @readonly = "readonly" })
            @Html.ValidationMessageFor(model => model.equipData.StartupDate)
        </td>
        </tr>
        <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.LastInspectionDate, "Last Inspection Date")
        </td>
        <td class="editor-field">
            @Html.TextBoxFor(model => model.equipData.LastInspectionDate, null, new { @readonly = "readonly" })
            @Html.ValidationMessageFor(model => model.equipData.LastInspectionDate)
        </td>
        </tr><tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.NextInspectionDate, "Next Inspection Date")
        </td>
        <td class="editor-field">
            @Html.TextBoxFor(model => model.equipData.NextInspectionDate, null, new { @readonly = "readonly" })
            @Html.ValidationMessageFor(model => model.equipData.NextInspectionDate)
        </td>
        </tr>
        <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.LastPhysicalInventoryDate, "Equipment Last Seen")
        </td>
        <td class="editor-field">
            @Html.TextBoxFor(model => model.equipData.LastPhysicalInventoryDate, null, new { @readonly = "readonly" })
            
            @Html.ValidationMessageFor(model => model.equipData.LastPhysicalInventoryDate)
        </td>
        </tr>

        <tr>
        <td class="editor-label">
            @Html.LabelFor(model => model.equipData.CurrentStatus_ID, "Status of Item")
        </td>
        <td class="editor-field">
         <div id="Status" class="data">
            @Html.DropDownListFor(model => model.equipData.CurrentStatus_ID, null, "Please select a value", new { @class = "dropDownStyle" })

            <a class="fancyboxEquip" href="../Status/Create"><img title="Click here to add Status" class="equipmentAddImage" src="../../Content/Images/add-icon.png" alt="Add" /></a>
            </div>
            @Html.ValidationMessageFor(model => model.equipData.CurrentStatus_ID, null, new { @class = "ui-state-error" })
           
        </td>
        </tr>
            
     
       <tr><td></td></tr>
              
        
         </table>
       
      
          <div id="customProp">

        
        </div>
       <input type="button"  />
        <input type="submit" value="Create" id="btn" />
    </fieldset>
}

<div>
    @Html.ActionLink("Back to List", "Index")
</div>

Here is the partial view that is rendered on via ajax on a selectedIndexChanged event. The important parts to note for me were: No form tags (everything seemed to work when i removed them, they were originally there from some messing around i had been doing), and setting the name of the textBox to be custData[+i+].Value

@model ZITS_BO.ViewModels.vmEquipment

<table>

@for (var i = 0; i < Model.custData.Count; i++)
{
    <tr><td>
    @Html.HiddenFor(model => model.custData[i].customPropertyName_ID) @Html.DisplayFor(model => model.custData[i].Value)</td>
    <td>
    @Html.TextBox("custData[" + i + "].Value")
    </td>
    </tr>
}
</table>

Here is the controller

[HttpPost]
        public ActionResult Create(ZITS_BO.ViewModels.vmEquipment vm)
        {

            if (ModelState.IsValid)
            {
                //Save the new equipment to the equipment table
                int newID = be.addEquipment(vm.equipData);
                
                if (vm.custData.Count != 0)
                {
                    foreach (ZITS_BO.boCustomProperties.ajaxPostData apd in vm.custData)
                    {
                        //Add the reponses to the customnameValues table with the new ID.
                    }
                }

                return RedirectToAction("Index");
            }

          
            return View(vm);
        }

The viewmodel is 2 partial classes, one being a list (custData). Hopefully this can help someone out