Unapplied Funds

I mistakenly did not select "apply all funds" when inputting a payment.  A bill was then sent out, which reflected this payment and showed a zero balance.  However, since the payment was not applied, the next bill incorrectly shows a previous balance .  I am not able to apply the payment now, despite my efforts - perhaps because it was billed.  Is there a way to override that feature so that the funds may be applied and the correct balance on the next statement is shown?