I'm designing a two PCB device where the PCBs are soldered together with board to board header. I have one PCB file for both boards, but a unique schematic sheet for each PCB.
I use unique net labels so the ERC does not claim I have an unrouted net between the two boards.
e.g.
"3.3V.a" vs "3.3V.b"
"MISO.a" vs "MISO.b"
It's messy and there's probably a simpler/cleaner way?