Yep, all you have to do is open up two instances of the VST instrument. I just did it to make absolutely sure, and it's happily playing away even as I write this.
All I did was go to "Devices - VST Instruments", selected Arturia Moog Modular for both #1 and #2. Then I went to the "Inspector Box" (the track listing column all the way to the left in the main Project Window) and selected "Arturia Moog Modular" for MIDI track 1 out and "Arturia Moog Modular V2" for MIDI track 2. There's probably a few different ways to get that same result, but that's the way I did it.
Oh, and I believe you need to go to the actual Moog Modular instrument windows to select the bank/ program (rather than using the drop-down box in the track- all mine will ever say is "default"). Don't worry, Cubase will remember which sounds you used for each track the next time you open the song.
Hope this helped!