Retroarch Aroma isn't on the Homebrew Store so if you want the latest builds grab the WIP build from the link from my signature.. but if your using Tiramisu Retroarch your better off using the Online Updater to update your Cores.
When it comes to the controller changes - you can use the "Manage Remap Files" option, that will save you controller changes.
For other changes - You can use the "Overrides" option, there you can save per Game or Whole Core Override.
(Both options can be found when when in the Ingame Menu)