I am struggling to make the purchase payment, now I have overdue all over but the invoice where paid, please advise, on how to allocate the payment from the bank to supplier accounts.

If I understand you, you are trying to make payment on a purchase invoice right?
Simply view the purchase invoice in question and click on new payment then select the paying account e.g Cash at Bank and click create. That’s all.

Kindly read guide for more information Record a payment | Manager