I need help repairing rust on a 1995 Chevy Silverado?

[ajdereicup]

I'm in the middle of trying to fix up the 1995 Chevy Silverado that I drive and I've run into a problem. There is rust all over the place but the only bad rust where it's all the way through is the top of both of the rear wheelwells. I took of the chrome trim and busted out all the rust that I could from the drivers side one (I'm doing one side at a time so I can hopefully use the other side as a guidline kind of when shaping the bondo). I then took a metal scraper brush and scraped as much of the rust off of the remaining metal as possible and then covered it with primer. I've been putting layer after layer of this bondo that comes in a tube thats already mixed and I'm almost done filling it out all the way.

But while I've been doing this I've been going around and trying to get rid of all the surface rust in other areas on it. I've been scraping the paint off of the spots where the paint has bubbled up due to rust and scraped as much of the rust off with the metal brush like on the wheelwells and then I have coated them with primer. Some of the spots are doing good but some of the other spots you can see the rust comming through the primer again and some spots the primer's actualy bubbling a little. So I was wondering why is this? Is this because somehow I didn't get enough of the rust out? Or is it because I'm not putting enough primer on it to keep the elements out? I'll try and add some photos later.

Thanks a lot in advance
Arthur