No - it's best from a corrosion point of view to use the same material as you are repairing (mild steel I'd guess). Stainless would engourage corrosion in adjacent metal, it's not so nice to weld, and there would be more chance of fatigue issues with the joints.
Some sort of rust proofing injection after the car is complete would probabaly be your best bet.
Spray or paint on a good coating of Zinc rich primer, such as Davids Zinc182 etc, on the back of all the repair panels and on the inside of the box section. It just fends of the rust and gives a bit of protection for a bit longer. And as Malcolm says use the same grade of metal as you are welding too.