I am not a midi expert a couldn't figure out how to do this. Could anybody help me out?

I’d be happy to... you can setup your MOXF and reface YC so that you can determine exactly which controllers are routed to the YC and which ones are not.

If I am guessing right, you are simply MIDI’d from the MOXF to the refaceYC, but it sounds like you are not using the MOXF’s Master Mode.
Master Mode allows you to address the internal MOXF on one “Zone” and the refaceYC on it’s own separate “Zone”. The advantage of doing this means you can determine which of the MOXF controllers influence the reface. You can deactivate specific controllers from affecting things on a per zone basis. For example, you would set the Zone Transmit Switch for MW = Off on the Zone assigned to control the YC.
You can activate and deactivate Zone communications with a front panel buttons.

The MOXF’s Master Mode lets you setup as many as 4 Zones. Each will have a set of parameters allowing you to customize what gets transmitted from each.

Before we go through the setup, tell us a bit more about what you’re playing in the MOXF and what controllers you do want the refaceYC to respond to... this way we can give you specific instruction. Master Mode is very flexible and therefore it would help to know if you are in Voice Mode, Performance Mode or Song/Pattern Mixing Mode internally on the MOXF Engine?

Let us know.

Thanks for your response! Presently, I use the Master mode of the MOFX only to set up my voices and performances in set lists. I did connect the reface YC via midi to the MOFX and connected the outputs from the YC to the A/D inputs of the MOFX. In the MOFX performance mode I created a performance without assigning any voices from the MOFX to it. That performance is reserved for the YC voice. When I want the YC organ sound, I go to this MOFX performance and turn the A/D input on. When I play MOFX sounds, I turn the A/D inputs off. So, the YC is always on the whole MOFX keyboard when I play it. The default midi controllers when connecting the YC via midi to the MOFX are the keyboard, the pitch wheel and the modulation wheel. The mod wheel switches the rotary speaker effect of the YC between Low and Fast and thats the control I want to put off. I don't use the YC rotary speaker effect (I use an external Lesly simulator). and would like to permanently turn it off without the MOFX mod wheel turning it on when I use it. I hope that makes things clearer and as you may see, I'm certainly not a pro midi user ...

Thanks for giving us an idea of how you are currently doing things.

Master Mode will allow you to setup a Zone that plays your Internal MOXF Program and setup a Zone that controls your external device (refaceYC). By giving it its own Zone you will be able to decide which of the MOXF controllers even get to address the refaceYC.

So you might still want to control the YC volume using an FC7 Expression pedal, but you can disable the MOXF from sending MW to the refaceYC.

Presently, I use the Master mode of the MOFX only to set up my voices and performances in set lists.

Excellent. We can show you how this would work starting from here.

The Master Mode has a second function (beyond the ‘set list’ thing). It is the Master Keyboard Controller Function that allows you to command 4 Zones.

In your setup, Zone 1 will play the internal MOXF program (Voice or Performance) and Zone 2 will be the external device (refaceYC).

Call up your first Master 001.
From the main screen press [F2] MEMORY
Here is where you are ‘referencing’ the internal MOXF Voice or Performance
Press [F3] ZONE SW (Zone Switch)
Set the “ZoneSwitch” and “ZoneKnob” to On
This activates the Zone function.

Press [EDIT]
Touch the Track [1] button to view the first screen of Zone parameters.
[F1] TRANS (Transmit) Set the “TransCh” = 1
Set the “IntSw” (Internal Switch) to On... turn the “ExtSw” = Off.
This makes Zone 1 exclusively in charge of your ‘referenced’ Internal MOXF Voice or Performance.
In fact, turn the INT SW On and Off to understand that this is the control to communicate with the internal MOXF sound.
Set it to On.

Press Track [2] or move the cursor right to the second slot (Zone 2).
Set a “TransmitCh” for the refaceYC
It can be any channel you wish. It will not interfere with the internal MOXF so it can easily be Ch1 or any you choose.
Set the “IntSw” to Off... turn the “ExtSw” = On
This makes Zone 2 exclusively in charge of your External Device (refaceYC)
And toggling the ExtSw On/Off makes and breaks the connection with this external device.

Press [F2] NOTE - here is where you can Transpose and region Zones to specific areas of the Keyboard, if you so desire. Yamaha uses the convention where “C3” = middle C

Press [F3] TX SW (Transmit Switch)
Here you can setup Bank Select/PC (you will not need to do anything with these) but cursor down on this screen to see the various physical controllers and an Off/On Switch for each. Cursor down in Zone 2 and set MW = Off
Review the controllers and defeat the controllers you do not want to affect the refaceYC...
PB (Pitch Bend), FC1 (Foot Controller 1, Sus (Sustain), FS (Foot Switch), Knobs, Assignable Function 1/2, Vol/Exp, Pan

Press [F4] PRESET (you will not need these; Bank Select / PC are not used by the refaceYC). You can, however, preset a Volume or Pan location for the refaceYC.

Press [F5] KNOBS each Zone has a set of Knobs. The default is the top Knob sends cc7 Volume, the bottom Knob sends cc10 Pan. On the left front panel Zone 1 and 2’s Volume are controlled by Knob 1 and 2.
Their Pan positions are Controller the lower row of Knobs 1 and 2 respectively.

Press [STORE] to update your Master 001

Since you are returning Audio from the refaceYC to the MOXF, you can easily defeat it Audio with the A/D In On/Off.

By adding a Zone Setup to each item in your Master Bank, you can customize on a per program basis what your Controllers are doing.
Hope that helps.

Thanks for your help Bad Mister! I did what you (very well) explained and it works perfectly. And I lerned a lot on the way!