Everyone's opinion is different and usually dicatated by climate and intended use of the bus.
My bus had the vinyl/rubber flooring glued to marine plywood that was nailed (
) to the steel floor. As good as I thought it looked, I pulled it all up anyway because I wanted to start fresh. I'm glad I did. Most of my floor is just painted steel, but the section over and around the rear axle was actually galvanized. Go figure...the galvanized part is where it jad some rust. I was lucky in that mine turned out to just be surface rust and a little wire wheel action took care of it. It was then coated with two HEAVY coats of a flat red oil based metal primer all the way up to the seat rail on the wall. The holes were filled with an outdoor rated liquid nails.
We then laid out a grid of 1x2 furring strips every 16 inches or so. These were glued down with liquid nails to prevent squeaks and secured with 20 year rated screws (lots of predrilling into the floor).
Between the grids we laid 3/4 inch (same as the nominal thickness of the furring strips) white rigid foam insulation. It doesn't have the same R-value as the pink stuff, but was cheap and I had a bunch before we started. We covered the whole thing with a 4 mil continous piece of vapor barrier.
On top of all that we screwed down 3/8 inch plywood. It is thinner than a lot of people would recommend, but is span rated for what it was on, has something under it in all places (foam doesn't compress all that much), and was cheap. The carpet was then laid on top of that.
All told I probably lost MAYBE 1/2 inch of headroom, but the floor has that nice home-like feeling now. No matter how you go, make sure you do it well because the floor is not the most convenient thing to fix after the conversion is done.