Some people won't like this answer, but if it is a trainer, jsut do the repairs then put some good clear shipping tape over the holes and fly. You will probably get a lot more holes before you are done with the trainer, and the trainer in my eyes is a tool to teach one how to fly, use and abuse

Another idea is to get stickers from differnt places, Futaba, Webra, OS, etc and put them on the wholes.

Jon