Emblems are the Aura's that rotate around your character. You can buy those from NPC Lowe in Ardeca using the Purchase Points you farm from DKSQ. Emblems are very expensive as they are an end-game item.
Gems are what you use in your weapons and armor. You can farm 7% gems also with Purchase Points at NPC Lowe in Ardeca.
7% Elemental Damage Gems are what you use for your weapons.
Medials go into your Pants (You can get these from Acquarai Ruins +87 or Arcadia boss drop +123)
All Resistance Gems go into your Armor (You can get these from Shadow Tower +95 or Arcadia boss drop +105)
Guard Bijou's are what go into your Helmet (You can get these from Shadow Tower +164)