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As silly as it may seem, I want to manually accept or deny affilliates as they apply. My system is intended to make high percentage payouts to affiliates that have a 501c3 non-profit status. The payments I make to the affiliates are donations to their cause, animal rescue/shelters specifically.

Also, I would like to be able to edit the emails the affiliates get when they first sign up. Or, have them land on a specific webpage when they register. Unless I can have some more options available. I want to give my affiliates banners but as it is, after they register they have to figure out how to find or where to go to get my link for there page. I would like to make it simple for them as "other" simular programs do to get the code. The only option for them that I see is a text link that says "Click here to visit...".

You could do that by asking prospective affiliates to contact you to apply, then once you've vetted them and accepted their application, you'd send them your sign-up link URL, or the URL of a "secret" page on your site where you have the sign-up link along with any other instructions/information/banners/etc. you may wish to provide to your affiliates.

If you create a page like that, you should also provide that as the "More information" link URL in your Seller Admin > Affiliate Program Settings; affiliates will be able to get back to that page by clicking the More Info button in their Affiliate Admin. You should also disable "List affiliate program in E-junkie Marketplace" in your Affiliate Program Settings, so existing affiliates in our system won't be able to find and join your program on their own.

We don't send any "welcome" message to affiliates, so there's nothing to edit in that regard. You may wish to read, and refer new affiliates to, our help page for affiliates that explains how our system works from their perspective:
http://www.e-junkie.com/ej/help.for-affiliates.htm

This help page for merchants explains how to set up an affiliate program and how our affiliate settings work:
http://www.e-junkie.com/ej/help.affiliates.htm