It's all about the affiliate.

If you're going to be running an affiliate program, golden rule #1 is that it's all about the affiliate.

Your mantra should be to credit an affiliate for a sale or lead whenever you possibly can.

Be competitive with your cookie length, work with networks that have multi-layer tracking, and ensure the conversion process is optimized from start to finish with the affiliate in mind.

Why?

well obviously, the better the product is optimized to credit the affiliate the more conversions the affiliate will see, and ultimately the more loyalty/traffic you're going to get.

on top of that, affiliates will pick your process apart. They're going to check cookies, compare data, and blame you for stealing sales, even if you aren't. so the less they can accuse you of, the better.