Whichever billing software you use for your business, it needs to be connected to a payment system of some sort which will process creditcards. Some people will do it 'in-house' but more often than not, they use a payment gateway service. I think this is the better option as it gives you access to better real time processing and fraud protection. Examples of fraud protection are IP checking, number verification, address checking - all done in real time. If the details submitted match up and nothing looks out of the ordinary the card p***es and is processed. If not, it's either rejected or flagged for manual verification.
Then after the card is accepted it usually goes through another stage of deeper checking, making sure the actual details of the card itself are correct (right number for the right name etc).
The advantage is two fold. First, you get less straight our fraud by people just typing in anything, and second it reduces chargebacks later on from people's actual cards being used by someone that shouldn't be using it. (ie. you lose it on the bus and someone goes on a spending spree later on).
Using a professional payment gateway, and to be seen using one, quite often deters people from 'having a go'. They'll usually try a soft target instead. No visible protection, no secure server etc... If they know you're serious about your billing system, they should know you're serious about hunting fraudsters down as well.
