Shoebooks payslips create a bill for each amount of super payable for each employee. The expense is recorded to 6-5120 and the liability to 2-1430. The system is designed to treat it just like any other accounts payable bill except instead of being recorded to Trade Creditors it is recorded to Super Payable.
In the reports menu you can run the ageing reports and select the Accounts Payable Account - Super Payable to see what is outstanding for each fund. You can also use the Payslip Super report in the payroll reports section to see what contributions are due for each employee / fund for a date range. When you want to pay the super you pay the bills just like a normal supplier. This assumes you are paying each fund separately.
If you are using a clearing house, the easiest way to do it would be to apply a bill payment for each individual fund and use the bank account called clearing account. When you have made all the payments you can, then do a New Batch Withdrawal in the banking menu from the bank account that you paid the funds and allocate it to the clearing account. The end result is that the clearing account will come back to $0.