You can pass the Affiliate ID along with the rest of the order information to the Check Out API.  The affiliate ID is associated with the EZ-Affiliate tool.  In order for this to feature function correctly you need to do the following:

1. Established your affiliates using the EZ-Affiliate tools. 
2. You must have a "cookie" set with the affiliate ID in it.  This is usually done in the link that brought the person to your site.  There is a small set of parameters that must be included in this link from the referring page.

One the affiliate cookie has been set, then you must add some javascript code to retrieve the affiliate ID from the cookie and assign the ID to the appropriate variable name.  See the code below.