I've always used sheet steel purchased at my local hardware store. I use a cutoff wheel in an angle grinder to trim away the rot. Then I shape the steel to whatever size and shape I need and weld it in. Multiple pieces of steel is fine as long as you're welding them in. On floorboards I generally don't bother grinding down the welds since there's a carpet going back over it. I use a mapp gas torch on steel before I paint it to get all the moisture out of it, of course only in areas that I can safely do so. I've had success using rustolium rusty metal primer and any color rustolium paint, with 3m undercoating on the underside.
It's a long time consuming process, but the results are worth it. And it's a whole lot cheaper than taking it to a body shop.
My cylinder head overhaul: http://www.jeepforum.com/forum/f13/cylinder-head-r-r-picture-heavy-1348138/
My transmission overhaul: http://www.jeepforum.com/forum/f13/how-change-transmission-electronics-1560948/