I’d use a Generic Remote map and bind some commands to arm/disarm tracks.
I.E.
- Set up several tracks pointing to different channels and/or plugins.
- Arm and disarm them as needed. You could do it with your mouse, or even build macros and bind them to key-commands, but I personally use a bank of MPC pads, plus a dedicated Generic Remote map, and treat it all kind of like organ stops.

My 16 MPC pads work in ‘track order’, and the pads are lit when armed, and dark when disarmed. Since these are using ‘note-on/off’ events to remote control the DAW, I set up a bank of MPC pads in ‘toggle mode’ so they only transmit on the ‘B port’ of the MIDI controller (MPK2 in my case). If your controller doesn’t have more than one MIDI port, then you’d simply set aside a MIDI channel that you’d never use for anything else but remote controlling the DAW and set your pads to use that channel.
You can record to many tracks at once, no big deal. If you later want to ‘freeze’ and then ‘merge’ tracks into one, again it’s no big deal.
Note, if you want to have a single MIDI event do several things in one go, just bind more than one command to the same MIDI event in your Generic Remote Map. I.E. Punching a single MPC pad could arm tracks 3-8 and unarm tracks 1, 9, and 10. Etc. It’s also possible to stack several Generic Remote Maps and use them all together at the same time (be careful though, and design things to avoid conflicts).
If you want to also ‘record’ any automation you do with a Generic Remote map, you can do it through a regular MIDI track using a virtual loop-back MIDI port (See here for PC, or here for Macs on getting a Virtual Port). For this to work you’d create a virtual MIDi port, make a MIDi track in Cubase set to only listen to the relevant MIDI controller, and forward the output of the track to that virtual MIDI port. You’d set the input of the Generic Map you wish to automate via sequence as your virtual MIDI port. Note, you’d need to keep the track armed for recording or monitoring pretty much at all times with such a setup or your remote events will never make it into the map. This can really come in handy any time you want to automate things in the DAW that don’t have dedicated automation lanes (such as arming/unarming tracks, launching marcos or logic editors, stopping the DAW, etc.) Be aware that if you use these sorts of tracks to ‘automate’ CuBase via MIDI…Generic Remote maps do NOT save with your project…they stick with your DAW setup. So, make notes in notepad, and keep an exported copy of the maps in your project folder in case you ever need to ‘reload and assign’ the remote maps in the far distant future.