I am also confused about this. I was about to type a new post similar to this.
I'm also a 1.0 player (with legacy) and I bought a physical copy of the collectors edition for PS3. I only put in the code today and in the middle of downloading the game as I type this. I'm worried I messed up along the way when I asked me to log into my Square Enix account when on the website to redeem a code for the PS3, to redeem a code to download the game.
Long story short, I feel very ignorant at the moment and is wondering if how or if it's to late to Link my PS3 purchase.