Hi Pete,
Welcome to the 5 star forums. We will try our best to help you get your arms around this thing called affiliate marketing!
Here is a very simple article I found for you on cookies and how they work.
http://www.100best-free-web-space.com/articles40.html
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Also, if you want to partner directly with a company that is not registered as an affiliate on one the big sites, what are best practices for auditing that you are getting credit for every referral/lead?
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I assume you are asking about partnering with a site that is not on one of the big networks, like CJ? Sites that have their own tracking or 3rd party software but aren't on the big networks are many times called "Indies." (get you up on the lingo!).
Well to get credit the company has to have some type of affiliate tracking set-up. Some programs are considered more reliable than others and the merchant needs to set it up right for it to work. One thing you can and should do is after you 1st set up links for a merchant, click your link to see if it tracked. (If it's not pay per click. Clicking own link could get you in trouble.)
The only real way I know of for sure to test, is to make a test purchase to see if it tracks. This is not always practical. Some affiliates add more than one merchant to test and see which one converts better. Sometimes you can find feedback from other affiliates on certain merchant that will give you an indaction. Sometimes you just have to trust.
Not sure there is any concrete answer. Anyone else have any feedback for Pete on this?