What you want to prevent is wood getting and staying wet, because that's what starts the rot.
Sealing the underside of the ply helps if most of the moisture is coming from below; if it's coming from above, it may actually hinder drying. Water generally flows downhill - floors rot due to trailer leaks letting water pool on floors under carpeting, not because of water coming in the belly pan.
I'd use either epoxy or several coats of good paint on the top of the floor; that's what you need to protect.
Now, since rust really attacks wood, I'd cover the top of the frame with undercoating or heavy tar before bedding the plywood down, and leave the rest of the wood open to help get rid of any moisture that should get in.
But treat the top of the floor - and keep an eye out for leaks. If you're storing the trailer for a while, consider taking up any rugs to leave the floor bare so it dries out more quickly.