The Organelle mother.pd patch merely provides a bunch of sends and receives between your patch and the hardware… most of the messages it sends to your patch are shown right on the main mother.pd window (notes, knobs, etc…). It receives message to set the led color and set screen lines on the OLED.
There are also a few other messages that have been added as the OS has been updated, and you are right these really should be better documented. Graphics messages to the OLED screen are detailed here:
https://patchstorage.com/graphics-demo/
There are also a few messages allowing your patch to utilize the encoder wheel:
[s enableSubMenu] -- send a bang from your patch to take control of the encoder
[r enc], [r encbut] -- receive these values when the encoder wheel is turned or pressed
[s goHome] -- tell the OS to return to the main screen for selecting patches and settings (since there is no dedicated home button, if your patch takes control of the encoder wheel, it must provide mechanism to return to main menu)
And there are a couple messages for disabling the default MIDI setup:
[s midiInGate] -- send a 0 or 1 to disable/enable mother.pd from receiving MIDI
[s midiOutGate] -- send a 0 or 1 to disable/enable mother.pd from sending MIDI