Silly question maybe but are the holes punched from the outside or the inside of the cap? Should the sharp little nipples that are created by punching the hole be up inside the lid or do they protrude down on the outside?
From a functioning stand point, it probably doesn't matter. I have never punched them from the inside out (sharpies out), alway outside in. If you have the time, I find drilling them (no sharpies) makes cleaning them easier when they get moldy.