You can't upload files via ajax, you need to use an iFrame or some other trickery to do a full postback. This is mainly due to security concerns.
Here's a decent write-up including a sample project using SWFUpload and ASP.Net MVC by Steve Sanderson. It's the first thing I read getting this working properly with Asp.Net MVC (I was new to MVC at the time as well), hopefully it's as helpful for you.