Using Javascript prompt you can not take multiple values.
For that you can use Jquery popup.
after adding jqueryui plugin you can use it.
like this-
<script>
function funShow() {
$('#dialog).dialog({ resizable: false, height: 140, modal: true });
}
</script>
<div id="dialog" title="Basic dialog">
<input type="text" id="txt1">
<input type="text" id="txt2">
</div>
<asp:Button runat="server" Text="Button" onClientClick="return funShow()" />
FOR EXAMPLE FOLLOW THIS
-http://jqueryui.com/demos/dialog/