if it's a cpo that has unpunched holes and you need to line the cpo up, what i do is cut out two button holes with an exacto knife, usually one on each end of the epo, than put buttons in and apply it, and then cut the remaining holes after.
edit - the only way you're really ever gonna notice an out of round cut is with a joystick hole, the overlap on the collar of the button will always cover it unless you seriously fuck it up.