Question about setting up affiliate program...

Overall goal: Set up a 1 or 2 tier affiliate program -- all auto-pilot -- that allows me to sell a 'real' cd product (not digital download).

This q might sound stupid.

I have found some fulfillment houses that will do the physical order filling + sending, etc.

What I want to know is, how do I set up + 'attach' a 1 or 2 tier affiliate program to the fulfillment 'system?'

Is the affiliate program just a function of the shopping cart system I choose?

The fulfillment houses don't seem to address this issue.

Any help to clear this up is appreciated!

Thanks!

-- TW