Am I right in thinking the website PID number is your tracking code on your aff links? If so does it matter if that appears on a site that hasn't been submitted to CJ? Will it still count? I have tonnes of sites, it seems silly to submit them all. Why don't they give you an overall PID? Or am i completely barking up the wrong tree?
It probably doesn't matter which of your PIDs you use, but it only takes about 10 seconds to add additional sites to CJ (and get a separate PID for each site) - probably better to be safe than sorry. It's at least worthwhile for tracking your sales.