How to use Control or Command for Cut-Copy-Paste
You don’t specify what software you’re using to create your virtual machines, but usually you’ll have an option in its settings to allow the VM to recognise both the command and CTRL keys interchangeably for the Cut/Copy/Paste keyboard shortcuts.

For example, if you’re using Parallels Desktop, you can customise your keyboard shortcuts by going to the Parallels Desktop menu in the Mac menu bar and navigating to Preferences → Shortcuts and selecting your VM from the list.

So I would check your VM configurations to see if you’ve got the option of doing this. Doing so means you can’t go wrong in your virtual machine.

In terms of the macOS side of things, you can refer to Karabiner (or, more specifically for macOS Sierra, Karabiner Elements) for some advanced  keyboard shortcut functionality.