How to paint on plywood floors?

You can definitely paint them! If it's raw wood, you'll need to prime the wood at least to block the tannins in the wood from bleeding through. BIN Shellac based primer is the best for that! Then you can either paint with specific flooring paint or you can paint with regular latex paint and use floor (water based) poly over the paint to seal it for durability and wipeability.

Plywood isnt meant to be used as flooring only as underlayment

Yes, make sure it's clean before you start. Use TSP if the floors have been walked on to have a good start. Prime with Kilz Original or Zinsser Shellac. Then paint with a floor paint. Then seal, making sure it is compatible with the type of paint you used on the floor.