Cheques issued to supplier - returned

Need advise
we issued cheque to supplier for the invoice , and some times they accidentally bank in before the date , the bank will return the cheque and after few days supplier will bank in again and get it cleared .
at bank statement we will see 2 debits for cheque and 1 credit for the cheque
at manager i entered as 2 entries as payments for the invoice and 1 entry under receipt to same supplier , at bank reconciliation its gets tallied but under supplier statement it shows as over paid,
how to resolve this .thanks

First, although I know it is common in some locations, it is very bad accounting practice to issue a post-dated cheque. In fact, in many jurisdictions it is illegal.

Second, in my opinion, you should not have created two payments in Manager, because you only made one. The fact that the supplier deposited it twice into their bank account is irrelevant. What the bank statement shows is reversal of the bank error, which does not affect your books, only the bank’s.

Third, if you are obsessed with making your records match the bank statement, both payments and the receipt (two of which are imaginary) must be posted to the same account and subaccount. That is, everything must be posted to Accounts payable >> Customer >> Purchase Invoice #. The fact that your purchase invoice shows as being overpaid suggests you posted the receipt incorrectly.