Could someone explain

Just to be clear, you don’t want to MIDI sync Maschine to Traktor, you want to run Maschine through a Deck of Traktor (like a CDJ or turntable) and use Traktor’s FX and mixer controls on the Maschine audio signal before it leaves your computer and enters the speakers?

Found this on NI Forums

Maschine – output to out 1/2, which i have plugged to my in1/2
Traktor – set Deck D to live input, getting source from in1/2

Traktor decks A/B/C are set to out 3/4, 5/6, and 7/8 respectively.

With traktor sending the midi sync signal (using midi loopback device), and maschine set to external sync i find i can sync it all up quite easily.

This lets me add synched traktor effects to the incoming maschine signal, and since maschine as an interface is predominantly handled by the external hardware, it doesn’t matter at all not being able to see its program window.

(I would probably run deck Maschine through 7/8 so as to keep A 1/2, b 3/4, etc)