I've made a few of my own door bottoms on a few cars, the ones I did were rusty in the inner part of the door as well. Its common to find rusty doors. Generally the bottoms of doors only have a slight crown to them and not to bad to form. The way I've done it Is to measure, or make a template of the shape of the bottom of the door, or use the old piece you cut off if there is enough left to it, and leave enough space around your template for the width of the flange that folds over the door. Cut slits the width of the flange a few inches apart then you use a duck bill pliers to form the bend for you flange and finish off with a hammer in a vice, or a good sharp edge to pound it over on. If you have a sheetmetal brake, even better. Drill out all the spotwelds holding the skin to inside the door and cut up how high you need.
I then welded the flange to the door in spots, and completely welded the seam on the outside where the new piece butted the old sheetmetal on the door, and welded up the slits I cut. Using door skin adhesive like brian suggested is an excellent way to do it though, if you can get the formed skins you need. No worries about warpage and less likelyhood of corrosion. You will just need to leave some overlap on the doors sheetmetal for the new piece to fit over. I would have just bought new doors for the bonneville I did the door bottoms on, but I needed all 4 and they were listed at 200 bucks a piece at the salvage yard, and who knows how much better they would have been. The first door warped a bit on me, but after doing the others on that car and then other cars after that, you learn to go real slow, weld only a short pass, let cool a bit and skip to a spot a distance from you previous weld and weld another short pass and so on and so on. Then you won't have to worry about getting a bunch of warpage out. They also make a heat sponge compound to control warpage (htp I believe has it) or soak some towels in cold water and lay them around where you are welding. I didn't use either of these, but went real slow welding them up.