Hi melrWA
Thanks for your post. As we're not accountants we're not permitted to advise which accounts to allocate those charges to, if you're not sure I'd recommend speaking to your accountant.
From a software perspective, the super guarantee amount should be processed through payroll by following the instructions in this Help Article: Checking and adjusting superannuation
The charges could be entered as a Spend money transaction.
Please let me know if you need further help.
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