Affiliate System

Question

Hello,

I am trying to get an affiliate system in place using PayPal and 2checkout. I am wondering exactly how the process should be. Here is an outline but I am not sure:

1. User enters via third-party-site and a cookie is set of that site (for lifetime)
2. User then pays
3. PayPal/2checkout redirect after payment to my site and then I update affiliate db

Sometimes after paying, the user does not click on the return URL. This can be a major problem as without returning to my site, I cannot say if the user used an affiliate or no. How do I get around this problem? Also is my cookie method the best method for this problem? Is the workflow correct? How do I integrate this properly with PayPal and 2checkout?

Thank you for your time.