1) Mark the S-16 as joint, which will create two separate Form SE for the self-employment tax.  That should result in just one F 569

2) Create the two separate Sch C's (which can be a royal pain), take the LLC designation down at the bottom of S-16 on one of them, and override the gross receipts amount on the F 568-IW (?) page so that only one is created and only one $ 800 payment is due.