To set up the control, you only need to hit the TAB button, got to controls and set/configure the next buttons
Back, Select and Custom1 (you could use 1 to 6, but only one is used)
after that go to Display, select any system that use this theme, and from there to layout option, just right there you can configure what custom button you want to use (from the previous step) to call the theme's menu (upper icons).
about the rest, well let see.
1. would there be a way to show the controls for the game...kind of like CP wizard? <- really dunno maybe it does but need time to search about it.
2. Any way to add the manual like on the nes mini? <- you can point me to an example here so i can check it out
3. How about changing the theme music/sounds for the different systems? <- Yes i can do that, the only problem is the size with all the images, systems and now a unique music for each system it could be a problem (a very simple example, 42 systems each one with a diff music of 1mb , well 42mb only in music
)