I'd be glad to help you match the payment to the invoice. Can you also tell us how was the transactions recorded? This is for us to make sure that we give you the right steps and information that are applicable to your case.
In the meantime, you can use the Bill Payment feature to apply the payment to the supplier bill. I'd be glad to show you how:
Open the bill or supplier invoice that you want to mark as paid.
Click Mark as paid in the upper-right hand corner.
Scroll-down to the Credits section and look for the payment, then check the box before it.