yo fragezeichen, yes very cool scenario.
realtime 64 bar recording of both units at once preferred, although bring up the volume of the track recording by all means, perhaps apply some peak style compression to even out the listening experience.
if i do a realtime recording of both units, that means the drums will be played by a single voice korg prophecy, so, the rhythm track might be pretty minimal, but with some realtime delay and reverb should be okay … also possible to p-lock the sequence using the Machinedrum midi sequencing capability.
it is okay to use a drum machine to midi-sequence the drum track, as long as the sounds come from a separate synthesizer for the drum track.
it is also totally okay to capture the 64 bar recording using an Octatrack as a mixer/recorder device only.