eBay is now being a bit selective on who they approve as an affiliate. SO I highly recommend you get you CJ account and affiliate account established before buying any tools to help market.
I don't think it does matter if all you are asking for is whether to sign-up as an eBay affiliate 1st or have a CJ account 1st. If you haven't had a CJ account and sign-up as an eBay affiliate, they would direct you to CJ where you would have to sign-up anyway. That being said, eBay does select affiliates based on their geographical locations.
I'm a huge fan of the eBay / CJ program and it has helped generate some excellent income for my blog. If you are rejected from the CJ ebay program, there are some alternate affiliate programs (PM for details)... It works if you aren't doing a BANS site and alternatively, write about ebay in your blog or want to promote the site. CJ is the best for ebay but there are other options if you're not accepted into the program. Good luck!
It seems Ebay does not allow affiliates from my country. I created a CJ a/c and got automatically immediately rejected by Ebay.
It really depends guys.. I was asking for eBay approval for over 1 year.. Well i used to work with them, then dropped me for some reason and some months ago i got approved once again. If they reject you just contact them! ATM making around 500 euros/day from them