We used small squares of sheet metal, glued in place with silicone. First, we sanded any rusty areas, swept/vacuumed, wiped w/mineral spirits, and painted the whole floor with rust-inhibiting paint...then patched the holes.
We screwed the plywood to the steel floor, after pre-drilling and countersinking the holes. Between the metal floor and the plywood is 1/2" rigid foam insulation and a 6-mil vapor barrier. If you plan to be in cold weather, and can afford to lose some headroom, I recommend insulating the floor as much as possible. Ours gets quite chilly.