Debuging a silverlight web created and used in SharePoint 2010 can sometimes make you want to pull your hair out. I literally knocked my head against the wall a few times trying to get debugging to work. It's pretty simple though, all you need to do is select your project properties, click the sharepoint tab, and enable silverlight debugger.
For more information please refer to http://vangalvenkat.blogspot.com/2011/03/how-to-debug-silverlight-webpart-in.html it is a great resource and helped me to debug my silverlight application.
Until next time, hope this post has helped you as it certainly helped me.