[Linda Buquet]

I've implemented it similar to what Chet said but didn't have a separate cart.

What I did when I managed Irvs Luggage affiliate program was...
If a visitor was entering the site referred by an affiliate or a repeat visitor carrying an affiliate cookie a line would be auto added under the phone number that said Priority Code 12345, with the number being the affiliate ID. So if it was a regular non-affiliate visitor nothing would show up under phone number.

Getting phone reps to remember to ask was a problem. But because we called it priority code it compelled some customers to automatically give it, thinking they needed it or it would help them get through faster.