In my experience running an affiliate program will not improve your SE rankings. Consider the following points.
1. Each affiliate will have an unique url to link to.
2. You have no control over affiliates participating in bad practices
The up side is in many cases a well marketed affiliate program will make you more money than good SE rankings. My advice: Get a domain for your affiliate program and one for your search marketing and put different looking sites on either.
I hope that answers your questions
