I was using Commission Junction for one website, and I decided to add one of my other websites (Account>>Website Settings). I was expecting some verification email or notification from them signifying approval of this second site, but I haven't heard from them all this time. Am I to assume that the second site has been approved, and any sales generated on the 2nd site (via the banners and links of advertiser programs I was accepted into for my first site) will count? P.S - My 2nd (new) site does appear in the "Select Web site" drop-down menu.
Try to log out and then log in again, add the website again. There is no confirmation email for adding other websites.