The VERY first thing I've done to both trac/kicks I've bought is to pull the carpet. The pad absorbs moisture and never lets it go ... If you insist on carpet, at least pull the carpet, strip away the pad, clean any sign or surface rust (with a little primer on the now bare metal), and put the carpet back without the pad.
I've been lucky that I didn't have rust issues (other than a spot or surface here and there).
For rust through ... there are 3 approaches
1) cut away and weld in new. This is the only proper way if the metal in question forms a structural part of the body.
2) cut away and pop rivet new metal. A decent way to get the holes covered. Use of seam sealer and/or fiberglass can ensure a completely sealed repair.
3) fiberglass patch the spot. This is a quick means of sealing it up, but you WILL be dealing with it again (especially if you didn't cut back to solid metal), since it's likely to continue to rust and/or crack.