Do I need to plan on 2 cards for every transaction with the ATF or once they have them I don't have to do it again?

Two cards every time

Just order a bunch from their website and you will always have them on hand and ready to print.

If you are doing multiple EFile Form 1s, you can get away with sending one set of prints along with multiple cover letters in the same envelope.

Also, if you file through Silencer Shop, once you scan your prints in through a kiosk, or you send them a set of fingerprint cards, they keep them on file and reprint them as needed for anything you submit through them.