With ASP.NET, how do I prompt the user for a yes/no question and getting the result back to my .ascx?
So far I can open a confirmation dialog with use of Javascript,
You need to use ajax, or to make a postback to the server. Your c# code is server side and the javascript is client side. If you use the ajax extensions for asp .net you can use javascript page methods:
PageMethods.YourMethod(confirm('your text'), OnSuccess, OnFailure);