javascript in ascx file

Is there any limitations in using javascript in .ascx files (user controls) I got it working just fine but some of the properties for objects, ie form.item property isn't coming up. I want to set a boolean var, set that to a hidden html element, then test it in the code-behind. I have attached the ascx file for reference.

What this is all coming down to is so I can have the user confirm a deletion in the web site, and then test for the boolean value. And since you can't use message boxes in ASP.Net this is the root I'm taking. Thought if there is a better solution in displaying a message box, I'm all ears, thanks.