I believe that the body does rest on top of the floor, You will want to raise it a little to put the new floor in. put a 2x4 (or 4x4 whatever works best for you and your jacks) between the jack and the body and gently raise it, put it on jack stands and repeat on the other side. I would recommend another set of hands and eyes there to help while raising the body, it's not light and there are a bit of parts that you need to watch to make sure you don't bend or break anything. I have seen people replace the floor in some older posts, they cover it pretty well.
