I had the same problem when I first incorporated a mixer into my small setup.
The first thing to realize is that the MNM has a pretty quiet internal amp. It is way less loud than the out out of say the Machinedrum for example. Youlol have to crank the main volume of the MNM up more, to match the output level of some machines.
Personally, I set the volume sliders on my mixer to be all the same level. This helps insure that your signals will all be loud enough to record. I set the internal synth machines of the MNM and MD to about 3/4 level, which leaves room for more volume within each track, if the need arises. If you start with all of your tracks being at max volume, then you have nowhere to go when it come to refining your mix levels. The trick here is to turn sounds down, to make room for the sounds that you want to be loudest (subtractive approach). from here you have balance the overall volume of each piece of hardware by fine tuning their main volume settings, and then usually more fine tuning of levels for each track.
This sounds complicated at first, but once you have your base levels figured out for each piece of hardware, you can leave your mixer levels alone, and pretty much just use the volume levels of the internal synth machines to find balance, rather than having all of your levels in flux all of the time. You need to set a foundation signal level based on the amp power/levels of your hardware, and don’t mess with it. Also, I find this approach gives me the most reliable distortion-free signal, and allows me head room for volume increases if I need.
As for the VOL parameter, I usually leave it alone unless I really need that extra boost or cut. To me, it sounds like the VOL parameter is doing something more than just increasing or decreasing the signal level.