Just mount the wheel or seatpost on the bike with the pitlock installed, insert the pit until it engages, then try to fit a 5mm or so allen wrench through the hole. If it goes through without pulling the pit off the nut, your golden - not work needed.
If it pulls the pit off the nut, or can't be inserted because of the skewer then either cut the end slightly proud of the security nut or flush with it.
It takes about 3 seconds with a hacksaw. If you leave it slightly proud - say 1/16" or so you still have enough meat to file the cut end smooth without scratching up the security nut.
I'm running pitlocks on my font wheel and my seatpost plus a security cable to help keep the seat from walking away.