Clearing overdue invoice that has been paid.

How can I clear an overdue invoice that has in fact been paid.  The invoice was paid in two amounts and I could not seem to match the two payments to one invoice, it just kept leaving the [age without matching both.  In the end I just created the two amounts separately from the bank feed so although the invoice has been paid it is still showing as overdue.  If I go to the overdue invoice and record the payment that way will it go through the accounts twice? Cant understand why it wouldnt match as I have done this before without problem.