Hi BnDM,
Thanks for your question. At the moment, there isn’t a way to manually mark super payments in Business Pro/Lite as Paid if they were paid outside of MYOB.
Even if the super has already been paid manually and the payroll expense has been recorded, the Super Payments report may still show $0 paid and the pay run can still show Unpaid. That’s expected if the payment wasn’t made through MYOB Pay Super, since the report only picks up super payments that were processed through MYOB Pay Super.
Cheers,
Princess