Invest in a can of POR15. In order to remove the rust underneath the undercoating, (assuming the metal is still good) you'll have to remove the undercoating, remove the rust with a grinder/ wire wheel if possible, clean it, and then apply POR15. After its dry, re apply undercoating.
Do you mean its rusted through the frame section that runs underneath the floor? That is a structural part of the body (correct me if I'm wrong) so if its rusted through enough the body will have lost quite a bit of support. Don't know if you can get that cut out and replaced or not??
I'd suggest removing all of the tar sections from the passenger compartment before you start. It has a tendency to hold completely rusted out floors together, giving them the impression of being ok. (plus they seem to hold water quite well)
Good luck, I've been in your situation before, I know how much it sucks.