You're referring to allowing the 2 CA 568 returns for the same file? 

I make a copy of the return, and uncheck the fed and CA EF boxes on the copy, leaving only the CALLC marked for EF.

Then I use that copy for the second LLC return only.   You have to uncheck the LLC box on the Sch C or Sch E for the first LLC, and check that box for the second one in that copied file.