I just discovered a way you can (sort of) do this. You can't deploy from two instances of Visual Studio to two instances of the same type of emulator, but you can deploy to instances of two different types of emulator. Although not without a small trick.
To see how this works, open two instances of Visual Studio, and open the same CF project in each. Next, you need to manually start two emulators. Find the file dvcemumanager.exe (it should be in C:\Program Files\Microsoft Device Emulator\1.0) and run it. To start an emulator, select it and then click Actions | Connect. For this example, start the regular emulator and the VGA emulator (and wait for them to fully come up, of course).
Back in Visual Studio, set one instance's deployment target to the regular emulator, and the other instance's target to the VGA emulator, and start each. Each app will be deployed to the appropriate already-running instance of the emulator.
You can't use this technique to run two versions of the same type of emulator, because there doesn't seem to be any way of doing that from the device manager interface. Also, you can't just start two instances of VS and set them to different emulators - I tried that and it doesn't work. For some reason the second one tries to deploy to the same emulator as the first, and you get the error you saw.