Yeap - think of it like an addon.
Here is my setup and Im lovin it so far:
(All before first booting)
Flashed my MG2 ROM
Flashed the Xperia Mod (I like some of the extra apps)
Flashed my Sense Mod (Again I like some of the apps)
Flashed The MOAR Mod
Boot the phone
Let it sit for about 10min
Now to re-theme the ROM
Reboot into recovery and Flash the MOAR ROM (The FULL ROM not my addon) (Acutally just start the Aroma installer)
Now dont flash the entire MOAR ROM - we are just looking at change the theme of our ROM to the way we want it.
When AROMA installer starts select "Run Morphology ONLY"
Pick a good theme and reboot to enjoy.
All of this has to be done on a fresh install correct?
