Ultimately this is your decision, our system does not lock you into any one particular billing method.
Our server software, cPanel, does have a full API so you are able to link your existing billing software with it, or write your own custom software. We would recommend using one of the pre-written billing systems designed for web hosting, which already integrate with cPanel. You can use WHMCS, which we feel is one of the best hosting billing solutions out there. On the Micro and Starter plans we will provide the license for a small monthly fee.
WHMCS integrates with more than 50 different payment gateways, such as PayPal, Authorize.net and SagePay so you can easily accept card payments online.