I keep looking everywhere but I can't find any material regarding Agi or Agi/Mastery for PvE. Mastery is great for poisons right and that's where we get our damage, so should I put Agi/Mastery in all red and orange slots?
Put in your character name and server. From there you can have it auto reforge your gear and automatically select your best gems. It's not perfect, but better than anything else out there other than your own SimC.
As for a quick cheat sheet:
Red: Straight Agility Always
Orange: Agi/Mastery or Agi/Haste depending on your gear.