I have worked with Commission Junction (CJ) as both a publisher and an advertiser for years. Personally I find the system somewhat confusing, and the GUI outdated - but - it does work, especially for certain types of affiliates/products. Here is the first in what I hope is a series of real world examples for publishers and advertisers.
As a publisher, I often want to link into specific products or services of an advertiser - not just their homepage or a generic topic page. Some advertisers make deep linking possible - and some don't. For those who do, these steps should help you out:
Log into your CJ account, and click on "Get Links".
Then click the "By Relationship" sub-menu - you should all the programs you belong to.
Click on the "View Links" or "View Products" link for the program you want to work with, and on that page find their deep linking option (note: this will only be available if the advertiser has made it so in the system).
Get HTML" - click on which ever you prefer.
When the window pops up, paste in whatever advertiser URL you want to link to in the "Destination URL" field (you should have their site open in another window with the page you want to link to) then click the "Update Link Code" button.
You will get a URL returned that is coded to that specific page, with the advertiser name as the anchor text (unless you change it first in the "Text Hyperlink" field). You can then change that to whatever you want, or, use it to make an image a link, etc.
Copy and paste the link code from the "Code" field wherever you want on your blog or website, but remember that linking to individual items may eventually produce a not found page when and if that item is out of stock.