Beatmaker's MIDI implementation is rather limited. The transport controls aren't controllable with MIDI. All of the effects, drum machines, and keyboards are but the notes and CCs are fixed, so you'll likely have to edit one of the QuNeo presets to match what you want to be controlling.
The Beatmaker 2 manual can be downloaded here: http://www.intua.net/support/
There's a section titled "MIDI" that goes through the setup of everything and has charts of what CCs are needed to control things.
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