Can someone please tell me what settings for Montage and Cubase I'm missing so that I can record some clean audio via the Montage A/D while midi is playing?

Audio will go only where you route it. So the short answer is you are having a routing issue.

When you say “all the MIDI playback is routing into the audio track”, this is because the audio is assigned to go to the same Outputs. By default, your internal MONTAGE Parts are routed to the “MAIN L&R” Outputs.

If you selected the "Quick Setup” template, “Audio Rec on DAW” without an understanding whether or not it is what you need, you are going to run into problems.

The “Audio Rec on DAW” specifically routes each Part to its own stereo pair Output. I’m sure I explained just how rare a situation it would be for someone to need a separate stereo pair for each Part, but because it is the scenario that, when needed, would take the longest to manually setup... that’s the reason the template does that routing. Most instances you will need to customize the routing to the current situation - which when you think about could be an infinite number of configurations. You just need to configure the OUTPUT routing on an 'as necessary' basis!

Audio routing, in your described situation, certainly doesn’t require each Part being routed to separate stereo pair. You need to route the MIDI Parts to the Main L&R, and then isolate your analog in to its own bus.

So you would need to customize the Audio template to suit your needs. That, is your only mistake... you thought the template was designed to playback MIDI tracks while overdubbing audio... and it is clearly NOT.

But your issue is easily fixed, by simply routing the MONTAGE Parts to the “Main L&R” Outputs
And route your A/D Input to a “USB 1-30” Output...

Let’s do this based on your description.
Part 1 internal Drum Kit
Part 2 internal Bass
Plug your guitar or mic into the “L” A/D Input jack.
You've recorded your Drums and Bass as MIDI tracks in Cubase...

Now let’s assume you go to QUICK SETUP and select “Audio Rec on DAW”
As described in the article, this reassigns the “PART OUTPUT” parameter of all 16 internal Parts...(it also turns OFF the Direct Monitor function) in addition to all the other settings it makes. You will need to reconfigure your Part Outputs to service your goal (after all you are not transferring 16 MIDI PARTS to AUDIO - which is expressly what that template is for)... You want to record the audio from the guitar or mic, discreetly, to an audio track in Cubase. You need to set that up... here's how:

Press [EDIT]
Press [PART SELECT 1]
The lower COMMON should be lit
Touch “Part Setting” > “General”
Set the “Part Output” = “Main L&R”

Press [PART SELECT 2]
Set the “Part Output” = “Main L&R”
Do so for each MIDI Part you used.
You will also want to hear these Parts so, the MONTAGE “DIRECT MONITOR” should be set to On.
“Settings” > “Audio I/O”
Set Direct Monitor = On

Next, let’s route yout guitar or mic to its destination... while in EDIT mode...
Press the upper [COMMON] button
Touch “Audio In” > “Mixing”
Set the “A/D In” top half of the Audio In screen
Input Mode = L Mono
Volume =
Set the OUTPUT SELECT = USB 1*
* you can do so by touching this box, to see the pop-in menu, select “USB Mono” > “USB 1”

In Cubase Pro 9.5
Setup an Audio Connection for recording
Go to STUDIO > Audio Connections > Inputs > click “ADD BUS” > add a Mono bus > Audio Device = MONTAGE > Device Port = USB 1

Return to the main Track screen.
Create an Audio Track set to get input from the “MONO IN” you just created.
When you activate the Record Ready (red) and Monitor (tan) you will hear just your A/D Input arriving on the Cubase Audio Track.

Almost there....getting lost in the routing the guitar section above:

I'm using a Multi/GM Performance template like you do in the videos.

After pressing the upper COMMON button on the Montage, I'm not seeing where on the screen the Audio IN - Mixing is. (I see on the far left column Home / Motion Control / Mixing / Scene /Play/Rec. The Mixing from this screen shows AD but not a way to select Input Mode.

Thanks!

I added screenshots while you were reading and posting...

After pressing the upper COMMON button on the Montage, I'm not seeing where on the screen the Audio IN - Mixing is. (I see on the far left column Home / Motion Control / Mixing / Scene /Play/Rec. The Mixing from this screen shows AD but not a way to select Input Mode.

You have to be in EDIT mode to see the edit options... you describe the HOME screen...

I've not found the way to that screen. Tx

From the HOME screen
Press [EDIT]
Press the upper COMMON button
Touch "Audio In" > "Mixing"

Keep at it...

That did it!

Thank You So Much!

Again!