The majority of rust problems are caused by either galvanic action or water soaked mud getting stuck in areas of the paneling.
Galvanic rust is created by the passing of currents through the panels because of a difference of electrical level between them or using the panel as a ground path for lights. It will usually start at a place where there is a spot weld and spread from there. The passing of current between them causes a gradual loss of electrons on one side to the other just like battery plates.
Contaminants like salt and mud stuck in areas also causes rust to start and progress. Ford had a very poor design for the mud guards in the rear wheel wells that caused mud and crap to be thrown up into the base of the door posts as well as areas of the rear quarter panel. That is where you will see a lot of rot starting on Broncos. Also unprotected areas that are not sealed like the frame will just rust because of moisture and contaminant exposure. Another way for rust to start and go undetected for a while is a painted surfaces that actually had rust before being painted and not properly treated ahead of time.
There are products on the market that can effectively seal rust and provide years of satisfaction if they are applied properly. In cases where rust is already serious you need to take drastic steps to stop it, such as cutting out the rusted metal and replacing it. In the case of seams, you need to determine if it is surface rust or metal that is starting to be eaten away. Sand blasting will work for removing surface rust but the surface needs to be immediately treated with a rust converter / preventer to seal and prevent further progress.
Good luck on your project. Here are a couple of products to consider
http://www.por15.com
http://www.rustbullet.com
http://www.hammerite-automotive.com/