I am planning on having a phone dedicated to my ioio board. I wrote a simple server app and client app to send commands over tcp. The phone would then control the ioio board.
You can connect your Android device to the IOIO either by USB or BT. There is no other option at the moment. You can always send "commands" to the Android device using some other means that are then relayed to the IOIO with either USB or BT.