Connect them with a MIDI cable would be one way.
Connect them via a computer would be another.
Use the Montage to trigger the reface YC alone
Use the reface YC as one of eight KBD CTRL Parts combined with Montage internal Parts in a Performance.
Run the audio output of the reface YC to the A/D input of the Montage - mix it with the Montage / route it to its own stereo Output.

The best way? Too broad a question to say which is the "best way". What do YOU want to accomplish?

I suppose what I'd really like to do is connect the Reface (whether MIDI or USB..) and set up a patch in Montage that would control the organ, which would be set up to the side of the Montage, that I could then save to my set list feature. Can I do something like that while still sending the audio output directly from the montage?

That would be my perfect setup - the Montage controlling the Reface YC from a patch in my set list, but where I would never have to actually touch the Reface YC, and the audio output would still go out through my Montage so I don't have to set up an additional line. Is that possible?

Hi, i used the Montage to control my Reface CP.
For midi connexion and select a part to control, suit the bad mister explanations.

You will need to touch the Reface YC to control drawbars, effect ... or you made your voices on the Reface YC, save them in Reface soundMondo on an ipad or iphone or ipod.

To load the voices you need on the reface it must be connected by usb with the good adaptor.to the iphone/ipad or ipod.

That what i done, in the montage performance when i need to use the Reface CP, i have a part with master zone activated to control the reface with the good midi channel, sending volume control change and note limit.
The iphone with Reface soundmondo app have a dedicated set list , i just need to press the good voice on the iphone to play with it from the montage.

I don't play the mini keyboard except to program my voices before to save them in Reface SoundMondo app.

That makes sense. Thanks Joel!