Yep, create a tracking ID for each site and when you create the aff links select the tracking ID for the site you want to track commissions.
You can create multiple tracking IDs, so that you can analyze orders coming from different Web sites. There is a limit of 100 Tracking IDs per associate account, but you can request more by contacting Amazon Customer Service.
Use TrackingID1 on Site Use TrackingID2 on Blog Use TrackingID3 on Forum and so on... You can manage Tracking ID's, but use them carefully as they can't be deleted.
its simple, you should create tracking id. contact your affiliate manger if you need helping doing it.