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You can only have one 568 return per client (annoying, I agree!).
What Ive seen some people do is make a copy of the file, and then on the copy, unmark the EF boxes for the 1040 and 540 and only mark the 568 for Efiling. Then file the first return with the 1040, 540 and first LLC 568, then use that second copy of the file to only Efile the 568 for the second LLC (does that make sense?)
You'll have to uncheck the SMLLC box on the Sch C that isn't being Efiled on each return.