Ohhh i thought you were running a full version of cubase. Yeah that's the problem right there Cubase LE is limited on the I/O. I had my first run in with LE4 about 4 years ago and it was only 8 I/O at a time. Cool for demos in the garage but not for full on production.
I would def suggest getting to know cubase if you don't already then throw down on the full version when you can. The extras are worth it.
For your input routing in the RME matrix just do a 1->1 set up. It should parallel the output assignments the whole way down.
Good luck,
-Casey