I don't think this is the preferred method. One project should be for one PCB.
If you have a single PCB that you want to split into two PCBs you might get away with it by adding notes to a mechanical layer that tell the fabricator to score the PCB so it can be split in two. There would be only the single PCB outline then for the combined boards. I have never done this though and I understand some fabricators may still consider it as two separate PCBs. Maybe someone else can comment? Or go ahead and try it. If you do split a single PCB it would of course have to have the exact same layer stackup, thickness, finish, etc..
