There is a web service called KashFlow
. Free 14-day trial and then it's $18.00 USD per mo. after the trial.
This software is great. It integrates directly with WHMCS via a module. Once the module is configured in your WHMCS it will run as part of the cronjob that WHMCS runs. It will copy over new invoices and mark them as paid.
It will also integrate with a PayPal account. I didn't get a chance to play around with this part of the integration much.
I really suggest giving it a good look over.