This is driving me insane, basically 8 years after your topic, that no one replied to. I want the same. What I want is the ability to use the MC Template with Maschine, as well as other custom Templates I made.... and sadly, this isn't possible because of midi port conflict.
To answer your question (not that it matters this late), you have to disable your Maschine in the MIDI Input section of Reaper's Preferences (Devices / MIDI). And also disable it in Outputs, if it is. Then, you can enable Maschine / Mackie Control as a Control Surface (further down in Preferences), and set the Input and Output ports to "Maschine In" and "Maschine Out" (whatever version of Maschine you're using).
Hope this helps... again, it's way late, but at least someone helped you!
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