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Do Masked URLs work with Affiliate links? I have a masked URL, that is masking the Affiliate code and I don't necessarily want people to see the ugly link with the affiliate number. Is this going to disrupt the tracking process? Thanks!

As long as the masked/shortened URL redirects to your full affiliate link URL, it should work fine. This help page explains how to get your link URL from the complete link code we provide in Affiliate Admin:
http://www.e-junkie.com/ej/tips.for-affiliates.link-url.htm

HMM... Well I did the link like it said. But if the masked URL redirects to the long URL, not the affiliate link, is that the problem? If so, wouldn't I need a separate masked URL for every affiliate? For example, my long URL where affiliate links are redirected to is http://dreampartner.acenter4growth.com/ I don't want people to see my regular website URL and go off looking at other stuff.
So my masked URL is http://AttractYourDreamPartner.com - It masks everything that comes into it through that long link. Should I redirect them to the shorter link instead?
I'm also trying to avoid people knowing that there is an affiliate program.

Aha, I misunderstood what you meant by "masked URL"; I thought you were inquiring about link-shortener services like TinyURL. The landing page URL does not matter for affiliate referrals, as long as the buyer was referred to your page through an E-junkie affiliate link and uses E-junkie purchase buttons on your page to place their order. However, the masking approach you're using can lead to other problems if you use our Cart buttons (our Buy Now buttons are not affected by this):
http://www.e-junkie.com/ej/trouble.cart-items-not-retained.htm#frames

Each affiliate gets their own, unique Hop Link code from E-junkie Affiliate Admin; they must use this link (or at least the URL of the link) to refer buyers to your site. These links will refer all buyers to whatever landing page URL you have set up for your hop links. Buyers who click a Hop Link will be redirected to your landing page URL while our system sets a cookie in the buyer's browser that expires in 6 months. Every product that buyer orders via your E-junkie purchase buttons during the lifetime of that cookie will earn the referring affiliate a commission according to your specified share percentage.

This help page explains our affiliate system and related settings in detail:
http://www.e-junkie.com/ej/help.affiliates.htm

We also have a help page for affiliates, explaining the system from their perspective:
http://www.e-junkie.com/ej/help.for-affiliates.htm