I've removed a top deck before on another boat and it turned into a big job to get it tidy again. I would encourage you to do it through the side as the above posts by experienced people recommend. The more worried about your fibreglass skills the more you should go through the inside of the hull, even if you don't do a very good paint job on your repair nobody will notice it but your decks everyone will see. If you do manage to buy a new deck you need to trust your resin skills to glue it down with absolutely no gaps anywhere or it will suck water and it is very difficult to stop these leaks afterwards