I actually found a big part of my answer in the manual! (audio section). Apparently there's an "audio map" that will let you send any channel to any channel. (Although I did not see mention of the M/S derived center channel that is mentioned in the audio overview).
If your sound is actually mono, the M/S option will not improve things. You need to choose at least 4ch under audio, as the center goes to channel 3, DCP-o-matic will automatically set channels 1,2 and 4 silent. It may be safer to choose a standard 5.1 channel setting, though, even with only channel 3 carrying signal.
For leveling, you should have the loudness analysis option enabled in prefs (R128/LEQ).
Then aim for a LUFS value of roughly -20 LUFS, or an LEQ(m) value of around 80dB. As a rule of thumb, -15LUFS is too loud, -25LUFS is too soft for most content. Always best to check in a theatre, but these values will get you into the right ballpark.
Your peak/true peak values should stay slightly below the 0dB mark, it doesn't matter if DCP-o-matic signals them yellow or red, as long as they don't hit the 0dB line.