I run a Dark Energy and Minitaur through a MD, and on the contrary, I find it adds more warmth compared to running them straight through the mixer. Sure you are losing analog warmth, but you gain digital warmth which in the case of the MD I find very pleasing!
The DE has a very hot output so I keep the amp usually from 5-7 (11-2 oclock), with input machine on default settings more or less. I adjust the volume from the input gain parameter on the first page if I need a hotter signal. Im not sure exactly, i just experiment and it has always worked fine. Try a resonant patch with filter movement on the DE and it’s pretty easy to tell where the MD inputs start distorting. I usually work around that range since I also really like the MD’s distortion.
Not sure if I can really help with input levels (i stick to the gate machine, or whatever the first input machine is), just wanted to say how good analog stuff sounds through the MD.