I just signed up for Commission Junction, mostly to do some eBay stuff, that I've been working on. In my application, I just stuck in the first URL that I though of, since the website where I'm planning on putting the links does not exist yet. Can I just go ahead and register any of my other sites in CJ, and stick links on any of them, or do I have to get each one individually approved? Is there any conflict having CJ ads and adsense on the same page?
"Is there any conflict having CJ ads and adsense on the same page?" Nope "or do I have to get each one individually approved?" I think you need to submit each page individually, most people don't though I dont think.
Each Advertisers will approve the site you applied for them. You can use any site at first and just add the rest. No there no conflict. CJ are not contextual ads