This help page explains our built-in affiliate system and related settings:
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
As explained at the link above, you can define a Common share percentage for all your products across the board and/or override that with a product-specific share percentage on particular items. Regardless of what kind of hop link the buyer followed, the referring affiliate would earn your product % on any purchased items that have one, or your Common % on all other purchased items.
You can also grant an Extra Percentage to particular affiliates; this would be calculated on the total price of all items purchased by that affiliate's referred buyers, in addition to any share %s that affiliate would normally otherwise earn. You can add this percentage and view affiliates in your program by clicking View/Edit Affiliates in your E-junkie Seller Admin.
Affiliates would join your program by clicking your sign-up link, which you can obtain from Seller Admin > Affiliate Program Settings. You can paste your sign-up link code on your site for anyone to join, or you can keep it secret and ask prospective affiliates to apply personally to have you send them the sign-up link URL if you approve.