I would use plastic backing as you do, and tiny plastic for the holes, rather than putty. You might have to reshape, but with some CA (superglue) it will make a much nicer filler. I messed up a bow limber hole, so i cut a small piece of styrene, CA-ed it in place, the refiled. Good as new and no flaking.
PE dedck - Eduard? Bear in mind it is POST WAR and not accuarte for a WWII boat...BUT, I would add the supports to the boat, then lay the PE on top of that, much like the real decks.