When you click on (in this case) a bank receipt to explain, the system will initially provide a list of recent unpaid invoices (against which you can allocate the money) and a list of invoices that have already been shown as paid but where the manual payment has yet to be matched to the bank statement.
If the sum you are trying to match is the same amount as any of the manually PAID invoices, it will give you the ability to reconcile it, ie match the sum in the bank statement against the manual payment.
In other words, you either explain the bank transaction by allocating it against an unpaid invoice or by matching it (reconciling it) against a manual payment already entered.
NB: If the system recognises the name on the bank entry (by say a rule already set up) then the dropdown list of customers will show that customer and so the list of unpaid and paid invoices will specifically relate to that customer. If it doesn't recognise it, and the drop down box is empty, then, unless you see the entry you want to use, pick the customer from the drop down list to refine the list.
Bit long winded but hope that helps