An affiliate only needs to click your sign-up link once and register for one E-junkie account for all their affiliate program participation (even if they also join other merchants' affiliate programs).
You may be interested in this discussion from our site's Community Forum which goes into more detail about how our affiliate system and the various link types actually work:
http://www.e-junkie.com/bb/topic/2690
This page explains the basic functions of using the E-junkie Affiliate system from an affiliate's perspective:
http://www.e-junkie.com/ej/help.for-affiliates.htm
You may want to click your own sign-up link to join your own affiliate program (your existing E-junkie login should work fine for this), so you can see in your own Affiliate Admin what your affiliates would see in theirs. You can use the Sellers and Affiliates tabs at the top of our site to switch between your Admin modes.