I have done this kind of work before.
Some hints: Find the best quality panels you can. Some of the repro stuff is not precicesly stamped.
Often, the new panels are MUCH bigger than the rusty area. Don't be tempted to cut up a smaller area than the panel. Those panels are intended to be installed full size since the welds go near a fold in the sheet metal so you get less warping.
Use a MIG welder to put them on, one spot at a time. Tack it on in 2 or 3 places far apart, then use additional tacks far away from each other. Dont do many welds in one spot all at once, or the metal will heat up and warp.
Also, try to do a butt weld, not a lap weld. If you must do a lap weld, flange the old metal so the new metal will fit flush. The Eastwood Co. sells a hand flanger, although you can get then that go on an air chisel which are much faster.
Above all, avoid warping the panel, this will minimize the bondo (filler) required later.
If you need bondo over any welded seam, use the fibreglass strand reinforced bondo, as its much less likely to crack than the regular stuff.