So let's say you have 10 domains and each have xx subdomains - would you have to add each and every one of them to CJ? Or maybe just the main domains? And what if I wanted to put aff link in forum signature or something, or in hubpages/squido/article directories
You don't have to add all websites on which you have your affiliate links to your CJ account, but it's good for tracking the sales - so that you knew from which site the sale would be.
Unless you have a high ranking inside of CJ this will just make you look like you don't know what you are doing. Advertisers want to see people/sites that will make them money. Plus it's a lot of extra work. Bottom line is you want your sites listed so you can appeal to advertisers and track results. Anything other than that is a waste of time.