Sounds like this is your first Skimmer install. The first is always fun.
In answer to your question, it is easier if you puncture the liner at the screw locations with an awl and then insert the screws. To make all of this easier. Clamp the liner to the front of the Skimmer at the top making sure that there are NO wrinkles in this section of liner covering the front of the Skimmer. Insert the awl through one of the corner screw holes on the top of the Skimmer face plate. Line this up with the corresponding hole on the front of the Skimmer and punch a hole in the liner. While holding the face plate, remover the awl and insert the mounting screw. Do not fully tighten screw. Repeat this process with the adjacent hole on the top of the Face plate making sure that the liner is wrinkle free. Continue this procedure with the remaining screw holes. Once all the screws have been installed piercing the liner, unclamp the liner and carefully back out all of screws so that the face plate will be free, making sure that all the screws are still piercing the liner. Apply a generous bead of waterproof silicone caulk around perimeter of the weir opening. Reinstall Faceplate and tighten all of the screws (Do not over tighten).
With your razor knife, cut and remove liner covering the weir opening. YOU ARE DONE!! Wasn't that FUN.