For the least hassle, PayPal's got a few options for payment. PayPal IPN can handle monthly subscriptions, and the service charges are not bad. You need to be diligent about moving the money out of the account, and about handling customer service problems.

Quickbooks is the default, but you can just keep a shoebox for your records and give it to your accountant every so often. You need a finance pro anyway, and if you don't have a founder who is an expert, outsource. You can't afford to screw that up.