This is the explanation per Bad Mister on the Yamaha Synth forum:
The CP4 Stage is a four Zone Master Keyboard Controller.
Like most keyboards the CP4 Stage normally Outputs MIDI data when you touch the keys.
MAIN - Channel 1
LAYER - Channel 2
SPLIT - Channel 3
Without any special setup, this is the normal MIDI I/O setup for the instrument.
If you are going to be using the CP4 Stage as the main Master Controller in a Stage Setup, it is highly recommended that use the MASTER KEYBOARD Function that allows you to create a four Zone setup that addresses devices connected via MIDI. These setups can be customized per Performance... so that when you recall a stage Performance the internal and external devices that you wish to play are configured as you require.
When you setup and activate the Master Keyboard 4-Zone Setup, it overrides the Normal Channel Output (which is three channels).