It wont even let you prepare 2 different 568's will it?

Its been years since I had this situation, but I think I remember doing a Save As and making a copy of the return, on the copy, you prepare the second 568 and then uncheck the EF boxes for the 1040 and 540, just leave the EF chosen for the 568. 

So on he original file, you EF the 1040, 540 and 568 for the first LLC, on the copied file you EF the second 568 only.....I think it works that way.