Okay for now my question is this, what do you put in the O's in your armor? o.O I see the orbs you can put in weapons from the alchamist but I don't see anything for armor. Am I missing something?

There's one's for armor too.. I think, honestly I wouldn't know o.o;

So I'm taking it their not implimented yet?

to put stuff in the equipment slots you need resonance stones.
http://grandfantasia.aeriagames.com/guide/item_storage#fort

Yes but is there armor ones? I have the magic ones for my staff/weapon but I see no armor ones.

Resonance Stones that can be put in armor usually have an (Armor Only) Note in there description, or its a Resonance stone that can be put in either Weapons or Armor. Resonance Stones that work with both appear to have a different effect for when in a weapon or in Armor.
Example:
Ice Vortex Resonance Stone:
In Weapon: 3% chance to add +15 Ice damage to your weapons damage on hit.
In Armor: +3 Ice resistance

I believe that is what the effects are. As you can see its capable of being put in both and likewise has different effects for each. There are many different ones and I doubt they're all store buyable =p.