The best way to kill rust is to cut away and replace any soft parts and sandblast all the pits in the remaining metal clean. Once you get that done clean the area with a metal treatment and then spray epoxy primer on it to seal it. You can put a thin coat of filler over the epoxy to hide any pitting.

So you don't end up doing it twice take a small mirror and a flashlight and look down between the trunk extension and quarter panel to determine if the rust is starting from the inside and working it's way out. This will give you a better idea of what, if anything, is hiding under the rest of the paint. Lots of times there is more rust on the verge of poking through and you may fix one small spot and eventually the rest of the stuff you missed will start poking through later on.