The Affiliates manager plugin can be integrated with the WP eStore plugin so that affiliate commission is given to the affiliates that send visitors to your store/site.
Step 1 (Install the Integration Addon Plugin)
Download and Install the WP eStore Integration addon.
Step 2 (Keep the Main Plugins Active)
Simply keep both the Affiliates Manager and the WP eStore plugins active on your WordPress site.
When you receive orders in the WP eStore plugin, the affiliate plugin will award commission to the appropriate affiliate (if the customer was referred by an affiliate).