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Hello Deanhowell,
If the regular payment you are making is for lodgements that have been recorded within QuickBooks Online, then just record the partial payments for the relevant BAS lodgement:
You will be able to match to these individual payments on the Banking screen.
However, if these payments are for a tax obligation not recorded in QuickBooks Online, I would advise speaking to your accountant or tax professional about how best to record it.
-Ken