Not exactly a thorough guide but the steps that I finally used to get my thinking working:
1. Download the latest IOIO library (currently 2.04 at time of posting - extract, and make sure the files are named as "ioio 20.jar" and "ioio20.xml" if not rename them
2. Download and extract the IOIO Workbench (currently 2.32 at time of posting, i think), that has demo`s for just about all the inputs and outputs you`ll want. You should be able to reverse engineer stuff from there...
Couple of other things I had to update the firmware on my IOIO board to work with the latest library, it shipped with Version 3, you need version 5. This link should help with that
https://github.com/ytai/ioio/wiki/IOIO-OTG-Bootloader-and-IOIODude
Lastly to make troubleshooting easier I installed a app from the Play Store called 'IOIO Hardware Tester' which helped my confirm BT connections etc.
Sorry, as my application was only controlling some LED`s with PWM output.
James