Your Affiliate sign-up link code goes wherever you wish on your site (or even on other sites, wherever you can paste HTML), as a link prospective Affiliates can click to join your program. The link will take them to register for an E-junkie login, where they can proceed to their Affiliate Admin page to Get Affiliate Codes, select you as their Merchant, and pick for which product(s) they want which kind of Affiliate link codes.
A Hop Link only redirects buyers from the Affiliate's link to your site where they would do all their shopping. The buyer still buys directly from you on your site, while the Affiliate earns a commission in the background for every product with an Affiliate share percentage set which that buyer purchases from you over the next 6 months.
A Direct Link provides a "Buy Now" button for instant checkout of your product from the Affiliate's link, so the Affiliate can market and sell your product in their own way from start to finish for you, without the buyer ever even having to know your site exists, but the Affiliate only earns their commission on each individual sale.
In either case, the buyer pays you directly for the full price of the product, and we calculate monthly lump-sum commission totals due back to each Affiliate, which you can pay however you choose (tho' we support and recommend automatic monthly Mass Payments via PayPal).
Direct Links tend to favor gung-ho Affiliates who are motivated to do a lot of marketing and selling for you, maybe even construct their own Web site to sell your product -- the more work they do for you, the more sales they can drive, so the more they can earn -- but more passive Affiliates who just want to network and refer sales to you in return for residuals may not find the Direct Link per-sale commission appealing.
Hop Links tend to favor more passive Affiliates who just want to network socially with people in-person and online, making more personal connections to refer sales to your site while they collect residuals for purchases their referred buyers make over the next 6 months -- the more people they meet and contact, the more they can send to your site and earn money -- but the more aggressive, hard-sales Affiliates who may want to control the full marketing and sales process their own way from start to finish might not appreciate that the actual shopping experience and purchases are happening on your site where they can't direct the complete customer experience.