The excess payments received from some customers were showing as negative balances in the Accounts Receivable.  I tried to move them to a new Account named Unapplied Payments (Other Current Liability).

I journalized each amount and then tried to set them off against the negative balances in A/R account. When I clicked the "Clear Payment", the whole invoice which had been paid, is being shown as unpaid.

Can someone please help me to understand what has happened and how to rectify that?