Self managed Super fund missed payment

We recently sent out a employee details update link and we were not aware if the staff member is with a self managed super fund that we need to enter these details again manually.  We need to pay the superannuation amount to the self managed super fund but not sure if we can pay directly to the bank account or if we have to undo any transactions in MYOB for everything to balance.  

Please help as this is the first time dealing with a self managed superfund.

Thank you