Post some pictures of the areas that need repairing. It will be easier to make effective suggestions that way. I just spent a bout 1 year going through my truck from front to back. In general, you have to cut out the old rusted metal and replace it with new metal. You can get replacement sheet metal form places like Jeff's Bronco Graveyard
http://wwwbroncograveyard.com or LMC Truck
http://www.lmctruck.com . Jeff's offers BZ members a 2% discount for all orders submitted on line. Enter discount code BZMEMBER an include your BZ User ID in your order.
Here is a link to my supermotors pictures of some of the body work
http://www.supermotors.net/registry/212/75692 this is one section of a main album of my 2009 - 2010 body work project. Unfortunately I haven't gotten around to adding captions to most of them yet, but you should get the idea. I either used metal from donor trucks or purchased some sections from the two places listed above. Instead of welding, I used structural epoxy, which is common practice in body shops now days. It is better than welding since welds are where the majority of rust starts.
Like I said post some pictures of the areas you are talking about and it will be easier to make effective suggestions.
Good luck,