For e-filed returns, you can pay your LLC fee electronically using Web Pay, credit card, EFW, or mail form FTB 3588, Payment Voucher for LLC e-filed Returns, with payment to:
Franchise Tax Board
PO Box 942857
Sacramento, CA 94257-0531
Yes, Form 568 doesn't account for the Web Pay method. You could enter the payment you made as if made with a Form FTB 3522 or other transmittal so that it is accounted for.