1. Gems and ore are required to enchant (Bezaubern) equipment.
Items have two different slots. "Veredelung" where you put in pre made +X items and "Bezauberung" where you can add enchantments.
2. You can't, but your Alchemist uses them automatically. When you have a new formula in your inventory it is removed and permanently added to the list of potions your Alchemist can make (At least your Alchemist in the Tower. Don't know if you keep the formulas from the Alchemist in teh first area)
3. You have to go to other people. But later you can instantly teleport directly to your alchemist who creates potions with herbs and other plants.