Hi!
The Atmegatron is monotimbral. This means that it only plays one patch at a time. The way the demos are made is by recording the synth into the DAW software, part by part. I don't know the NI Maschine software, but I've just had a quick look at the website and this is definitely possible. So the basic process is:
1) Create new sound on Atmegatron
2) Create a MIDI track and record and edit MIDI notes
3) Playback MIDI track while recording onto audio track
4) Mute the MIDI track so that it stops triggering the Atmegatron
5) Save patch on Atmegatron, just in case you need sound again (see manual for how to do this)
6) Back to step one!
The Atmegatron pushes the Atmega processor to the absolute limit just to generate one sound. You'd need more Atmega processors to play more than one sound at once.
If you're using a modern DAW (like Maschine) there shouldn't be any need for it to be multitimbral. If there's a specific thing you want to do that requires it to be multitimbral, let me know and I may be able to think of a workaround.
cheers
Paul

P.S. the current version of the Atmegatron software (v1.1) only responds to MIDI channel 1. v1.2 is still being beta tested, but it will allow you to choose the MIDI channel