Steve, you'll for sure want crossmembers for the seat bolts to go thru. I do it this way so that I can use thinner (20ga.) steel for the floor. Being thinner it's lighter and easier to work. When doing the crossmembers, try to work in an X or two for bracing. An X is still the strongest shape for strength. If an X doesn't work well into the structure, a triangle is the second best choice. Also, with an X or two again you can use smaller sized tubing for the X-members. I use 1" X 1 1/2" rectangular or 1 1/2" round. Have to finish up installing the boxing plates and start on crossmembers for the Plymouth frame this week, looks like we're about the same place on frame work though I still have to fit the engine and transmission and build some mounts.....
For body bolts, you have a couple options. either leave a notch in the boxing plate where the body bolts go and install a piece of channel between the frame and the boxing plate where the bolt goes, or weld a nut on the inside of the frame rail where the body bolt goes, then install the boxing plates.....