As much as I understood, razor's
@Html.CheckBox("myInputName", false)
Will create HTML like:
<input id="myInputName" name="myInputName" type="checkbox" value="true" checked="checked"> <input name="myInputName" type="hidden" value="false" checked="checked">
If you want with jQuery to select just input which is not hidden, use following code:
$('input[name=myInputName]:not([type=hidden])'