Prepayment is just a forward payment and should have nothing to do with GST other than people who do Cash Accounting for GST which would be .0001% of customers.

The entries for a pre-payment should be against a Journal where there should be a pre-payment option (system generated), this should post against the Customer and the balancing side would be some Balance Sheet account for Pre-payments (setup on the Customer Posting Group),

Everything else about the Pre-payment needs to be paid and the pre-payment is taken off any amount owing on the invoice is still valid.