The software only allows 1 568 to be attached per 1040 (ridiculous, I know).
You can use Save As and save the 1040 as a different name, then uncheck the EF Boxes for everything expect the 568, then use that copied file for the other Sch C's 568. That should give you 1 -1040, 1 - 540 and 2 different 568s (one in each SSN) in the EFCenter.