You can collect a Mystery Chest once the you have 100 Vision Vapour, an icon will appear, prompting you to collect.
If you run short of Spell fragments for crafting, you can disenchant things into Spell fragments...click on the green + button.
The Magic Academy is, to me, an awesome building. Upgrading it to the maximum will reduce production time for Catalysts, etc.
More information on the Magic Academy can be found here: