It will all depend with your workflow and style of making tracks. I usually start off with a basic beat and chords then I add melodies. Then I alter them to make verses and choruses. Fruity loops is great for doing this. You might find it easier to build drum tracks on FLstudio than on your Motif. Or you can save it as midi and play it back on your motif then record as audio into cubase.
In my opinion, Cubase and Motif is self-sufficient. Motif has great sounds so you really don't want to use it as mere controller.
The way I would do it is:
1. Create drum tracks on FL and render to .wav file
2. Upload the .wav drum track into Cubase
3. Record synth sounds from Motif into Cubase as audio
4. Mix it all down in Cubase.