MC11 is *very* good at making use of different outputs for zones. I run three output zones currently, using the on-board audio and two external mp3 soundcards. One feeding an amp via spdif optical. Works great. Better still is the fact that regular windows audio output (beeps, alerts, etc) all go to the right output without any contention from MC11. As in, even when MC11 is playing something the OS can still beep on that same channel. This is both good and bad, of course, but it's a sign that MC11 is taking effective advantage of how windows itself manages it.
What this may mean in your situation is that if your card can treat each output as a distinct windows device then MC should work fine. But this is a feature your card would have to possess and isn't something MC (or any other program) can work around unless the card has it. It may be simpler to just put a USB sound card on it and let MC use it independently of whatever MCE is configured to use. Something like Creative's USB MP3 can be had for $25-$40. Things like Audigy, Extigy, Edirol, Sonica and others can be had albeit at a greater price. Regardless of which one you chose MC will support using its output(s) indepdendantly.