Hi Rasmus,
thanks for your interest in MIR (3D!)! :-)
I used several approaches for both Auro 3D and ATMOS in MIR Pro. The most obvious one: Use the main microphone for the lower "bed" and add a second pass to your mix from another (preferably more elevated, most likely "wet only") microphone position in the same Venue. Typical example: The monastery church of Pernegg, where Mic 4 is high above the others. - Truth be told, I've even successfully used a mic a few feet behind the main mic (without elevation) for the top layer. 8-)
Another quick'n'dirty solution is to use a 3rd-party upmixer (such as Nugen's HALO) to virtually create the missing channels for the top layer.
... but don't despair - an actual solution for these (and many other) questions is on its way. :-)
Best,