I don't think "conflict" is the right word. It should be possible to create a configuration of commands that will work well for both. I suggest you start by creating a new install (in a new empty folder) just for testing the default MB3 configuration that we provide by itself. There may be some command overlap such as navigation, play/pause, volume etc. In that case it obviously makes more sense to keep those WMC commands (and remove the corresponding MB3 commands) since the WMC commands should (in theory) work everywhere, while the MB3 commands would only work when MBC is active.
It is still early days and we're trying to get the core API client stuff sorted out first and there are a ton of MB clients so if you want a mixed configuration you are essentially on your own for now.
