Im just starting my own program and im going full balls with NATS straight away. I dont want to fuck with the hassle of moving from ccbill to NATS. Plus I feel NATS shows your very serious about your affiliate program and ready to do business. Another reason I went with Elevated X CMS and Mojo Host because I know my stuff will be top of the line.
About cutting your own checks, my solution to this is im going to use Webmasterchecks.com Some time along I may send out my own checks but in the start when I have plenty of other things to take up my time and no billing department, WC will do just fine.
I think its like ~ 3 dollars per check they send out but if you split that fee with your webmasters then theres about no way you could do it any cheaper.
Just my opinion.