Update:
Ok so I refunded Heavensward through steam .. luckily it went through.

Then I went to the Square Enix store and bought Heavensward collectors edition PC download (it was cheaper! and I got the CE lol)
Added the CD-Key to my account and BAM.. got a notification after I started FFXIV:ARR (through steam mind you) and am now downloading Heavensward.

I still feel my account and how it works is a little wacky but.. as long as it all works. Also I guess if I ever uninstalled and reinstalled FFXIV:ARR from steam down the line .. since HW is registered under my original account it will auto download ..weather I get the standalone version from square or steam .. its .... lol really weird its like I have two copies of FFXIV:ARR one on steam, and a standalone from square. Yet the CD-key for the one on steam is being used by my friend.. *brain explodes*
However I feel all this could of been avoided if Square just made it possible for all CD-keys for FFXIV:ARR and HW to work weather you bought them from steam or squares store..