Sounds like you're describing "turning off" MIDI going TO the Montage 6 which implies it's the Montage you want to silence (not layer). If that's the case - you could connect an expression pedal to Montage's FC1 (Foot Controller 1) port. By default, this will act as a swell pedal and full heel will "silence" the Montage.

Can I use the foot controller on the CP88 to turn on or off the midi when I don't layer the sounds, or can I simply use the volume pedal to "bring in" the layer when I want it.

No to the first part, yes to the second.

A Foot Controller like the FC7 plugged into the CP88 sends MIDI CC (Control Change) messages. It cannot turn OFF the media it uses to communicate. That would be illogical. How would it then turn back On? But we understand what you are looking for...

You can use the FC7 pedal, sending CC7 Volume or CC11 Expression to "bring in" the layer when you wish to play both. To do so you need to recall the C7 LIVE SET SOUND, and activate the Master Keyboard function.

_ Press the [SETTINGS] button.
_ Use the Encoder dial and the [ENTER] button to call up the item you wish to edit. -- In this instance "Master Keyboard"

Please see the CP88 Owner's Manual pages 33-35 for how to activate a ZONE and then program what you wish that Zone to do.
You will see the Zone Switch (first of four possible Zone setups), activate ZONE 1
You can set the CP88's Zone 1 to Transmit Channel to match your external device (when playing MONTAGE from a Single Channel, you will want to set the "MIDI I/O Mode" of the MONTAGE to "Single" or "Hybrid" and select a Channel on which you will control it).
Go down the list of parameter settings you wish to use to address the MONTAGE... you can send a Bank Select and Program Change to the MONTAGE
Preset a Volume, etc., etc.
You also will be able to have it respond or not to your Foot Controller 1 and 2, as you may require

When you [STORE] your CP88 Live Set Sound - it will keep your setting that will cause the MONTAGE to behave as you desire.

If you get stuck, post back here.

Extra Credit:
When transmitting to the MONTAGE from an external controller using a single MIDI channel, you can set the MONTAGE "MIDI I/O Mode" so that it can receive data on a single MIDI Channel... This allows you to play even Multi Part MONTAGE Performances from a single set of keys on a single MIDI Channel.
Press [UTILITY] > touch "Settings" > "Advanced" > set the "MIDI I/O Mode" = Single and select a communication Channel