Well Bro, I dont think there is a "Proper" way to hook-up/connect a home based studio... So with that you should connect everything to YOUR comfortability...
But, what "I" would do is this...
Connect the MPC to the Digi 002 rack (stereo L/R) using the first two channels.
Then I would connect motif to the Digi002rack (stereo L/R) to the third and fourth channels.
As far as the midi goes, I would connect the Motif to the Motu128 in the 1st midi channel...(connect both in and out)
Then connect the motif to the Motu128 to the 2nd midi channel (both in and out)
This way you have connected both the Motif and MPC through midi and audio...
I hope I didnt confuse you, if I did, just ask me to clear up what I confused you on...
HOLLA
CATRON/TheReturn