If you want to check a checkbox in a particular row, find the CheckBox you want to check using FindControl method of the that Row and set its checked property to True.

Protected Sub Button1_Click(sender As Object, e As System.EventArgs)
        Dim cb As CheckBox = CType(GridView1.Rows(0).FindControl("CheckBox1"), CheckBox)
        cb.Checked = True
End Sub

The above code checks the CheckBox in the first row of the gridview. If you want to check CheckBoxes in all the rows you can do it in RowDataBound event

 Protected Sub GridView1_RowDataBound(sender As Object, e As System.Web.UI.WebControls.GridViewRowEventArgs)
        If e.Row.RowType = DataControlRowType.DataRow Then
            Dim cb As CheckBox = CType(e.Row.FindControl("CheckBox1"), CheckBox)
            cb.Checked = True
        End If
    End Sub

Please note: "CheckBox1" is the ID of my check box in ItemTemplate