There is a chest in the master's chamber where you can store things (and there are a couple items there you will probably want to use). Take the elevator platform down behind the throne, and it is on the left hand side after you go through the dining room, in an alcove.
You can right click most things in your inventory and send them to your battle tower chest (can not do so for quest items, etc).
Your enchanter and alchemist can use any ingredients from the chest; charms must be in your inventory to use. If you talk to your enchanter, alchemist or necromancer and go into their respective functions, any formula or creature parts left over after that are duplicates, and can be sold.
If you talk to your enchanter (or just use the machinery yourself) and remove an enchantment on a piece of equipment, you will recover that formula, if you don't already know it, and (with the required ingredients) can add it to other equipment with an open enchantment slot.
If you run out of most alchemy and enchantment ingredients, you can send your battle tower servants out for more (you'll have to get malachite gems yourself, required for many level 10 enchantments and any level healing aura enchantment).
Runners and Tower ?Very low success rate with Fanny Blossom?