hey darren

You can try one shopping cart, infusion soft or amember pro or butterfly marketing script.

Selection depends on what payment gateway you want to use. Say if you consider paypal , if you generate many sales, paypal will block you if you are generating big cash for the first time and they have a poor support , before you can explain them you would have lost a lot of sales and reputation.

If you have decided to go in with clickbank , Its the safer option with respect to payment processing and sorting out the affiliate payments automatically. But because of the affiliate theft involved with clickbank you will lose many JV partners here. Also the refunds. There will be many refunds in clickbank because there has been lotta product launches in the recent times and people been promoting similar kind of products to the same list again and again. Its has reached a saturation. so people have started buying a product and getting refunds and getting refund from clickbank is that easy .

So decide on a payment gateway first . Its also good to have two payment gateways like paypal and authorize.net so just in case there is a problem with one the sales is not stopped.

Apart from this most of the software manage the affiliate links, cookies and one time offers etc. commission tracking etc.

let me know if you have any more queries.

Cheers
Karthik