There is only (1) hole. I used the wrong drill bit from the underside to conceal wiring in a cavity for the taillights, and the bit caught and sent it right through the top lid/deck of the trunk and created the hole in it.
I only had (1) leak on the thing because I was missing taillight nuts so the seal on the center tails weren't tight. I then took some of the nuts off my second set of center tails to fully tighten down everything and no leaks. If you have a good set of taillights and all the nuts then it seals perfectly.