The Html.CheckBox() helper is not meant to be used in a loop. For this, write the <input ... /> tags manually. Your action method will receive a string array containing the checked values.
For example, if you had:
<input type="checkbox" name="theBox" value="foo" />
<input type="checkbox" name="theBox" value="bar" />
<input type="checkbox" name="theBox" value="baz" />
Then your action result would look like:
public ActionResult SomeMethod(string[] theBox) {
// if only 'foo' and 'baz' are checked, theBox will be a two-element
// array containing the values 'foo' and 'baz'.
}