"What are my options regarding affiliate programs with the shopping cart software ?"

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Short Answer:

You have the option of using the shopping cart's built in affiliate tracking, or you can connect it to a third party affiliate program, some of which are already integrated into the cart. Many affiliate tracking software and affiliate networks do not need special integration with the cart, which is why you don't see a lot listed there. If you need to find out whether a certain affiliate software/network is compatible with the cart, please contact us. Please see the related questions below to learn about using the shopping cart's internal affiliate program.

Developers note: The cart can post various data in the checkout as is required by most affiliate tracking software. This includes Javscript, posting the order variables to the recipt page, and using a silent post to send that info to a third-party system.

Detailed Explanation:

The built-in affiliate tracking system is simple and straight forward. The advantage to using third-party affiliate program software is two fold:

First, many of them have the network of affiliates. This is why big names like Commission Junction can charge several thousands of dollars just to sign up with them.

The second reason is that many of those programs are highly customized to different merchants needs. For example, the cart has only one level of commissoin payout. Some third-party affiliate software will let you setup several levels deep (which is not typical), and set up more varied payment structures. Of course, using the shopping cart's built in affiliate program may not cost you extra though, which is a great benefit to you.