Normally, the B/E boarding pass for your international segment is your CRC pass for all (domestic) segments of the itinerary.

In your case, with the stopover, show the CRC agent your itinerary and domestic boarding pass and explain your situation. Worst case scenario is that she will make you wait while she actually checks the system to confirm your B/E status JFK - ATH; I'm quite confident you'll get cheerfully waived through.

Assuming you have no stopover on the return, your ATH - JFK B/E boarding pass will be your "CRC pass" for the duration of your domestic itinerary.