On fiberglass you want to tape the entire area that you will be drilling thru with blue painters tape to avoid uneeded scratches and possible slips of the drill.

Once you figure out where you want them to be, I suggest that your friend sits in the yak and tries to grab the rods from behind him first, you want to use a hole saw. The hole saw is a 2 1/8" I think and should just be slightly larger then the diameter of the flushmount and then you will have to elongate the hole slightly and make it an oval. Take you time doing this as you do not want to go to big. Maybe a file or some sandpaper or smaller drum sander attached to your drill.

Take your time and put some thought into the angle and position of the flushmount before you drill, once you drill your locked in to a hole in your yak.