I've found that many independent paysite owners don't understand the simple concept of having two tours. A non-affiliate tour, linked from the domain root, with all the typical link trades, links to clip stores, etc. Then a separate tour that is nearly identical for their affiliate traffic, but without the link pages, clip stores, and any other external links.
I also agree that it's not a good idea to launch an affiliate program along with the launch of the site unless you're already experienced in building your own traffic and fine tuning tours. Having a substantial non-affiliate income is critical for an independent site to survive, otherwise the margins are just too tight to justify the time and effort needed to maintain the site.
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