Thank god the car's CAS system knows which one it is...even if the owners don't.
You can identify which key is key 1 & key 2 (or use other symbols) using the key labels available from the part database. So if you have two remote keys with two different M1 & M2 settings...then you should do something that visually identifies each key so that each driver will know what key they've picked up and if they may need to use the memory buttons on the seats:
See item # 8 in the illustrated diagram below: