So to rephrase the answer a bit, AIUI, Form 3522 is the voucher that credits the LLC with the $800 that is owed per the Form 568. Any more tax due above the $800 is to be submitted with the Form 568. Looking at Form 568 as completed by TTH&B 2016, I found the Tax Payments Smart Worksheet block where one can take credit for payment that was submitted with FTB 3522 and others. This changes Line 18 of FTB 568 to $0 for SMLLC that don't have additional taxes & fees for the year but TTH&B never asked this question in the interview sessions that I recall. Nothing about taking credit for this appears in any of the Step-by-Step views. This appears to be a bug in TTH&B when dealing with state requirements. The failure to E-file FTB 568 with individual returns even though FTB requires this form to be submitted electronically is a deficiency in the TTH&B product. Woe befalls the user who doesn't review the forms directly to correct the entries before submitting them for E-file. This is why I no longer use the TurboTax Online product. TT has screwed me over for 2014, 2015 and now 2016. Fortunately, after contacting California FTB today I won't owe penalties since I had manually submitted FTB 3522's for those years and only owe them the Form 568's.
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