Hi Christian,
As a fellow Reaper user, maybe I can help.
If I understand you correctly, you can do it as follows:
1. Set up your Vienna Ensemble instance with all of the instruments assigned to various channels as desired.
2. Open the I/O routing window (on either the Vienna Ensemble track or one of your destination instrument tracks). It should be on the track control panel. In the default theme, it should appear as a square "I/O" icon between the track name and the track fader.
3. For argument's sake, I'll assume you opened the I/O on the Vienna Ensemble track (it is easier to do many at once that way).
Under "- Receives -" click on "Add new receive..." and select your other track with the MIDI on it. If you do it from the MIDI track instead, you need to do the same thing but under "- Sends -".
4. You should now have additional options appearing just below the menu you clicked on. The one you want to focus on is the MIDI (bottom right) part. Change the destination channel to the relevant channel you would like to use in Vienna Ensemble.
5. [Optional] If you like, you can also click on the left Audio menu (probably looking like "1/2") and choose "None". Then the MIDI icon turns green, which tells you it's a MIDI-only connection. This step is entirely optional.
6. Add another Receive until you have all of the tracks there.
Then you should have instruments happily feeding MIDI into Vienna Ensemble.
Please let me know if you have any problems. It should be fairly straightforward once you get the hang of it, as Reaper's routing is incredibly flexible and powerful.
All the best,
Julio