Hi there,
to my understanding, the only way is to use one of the 6 matrix places for every part used.
Example:
- Slot 6: Source=Mod Wheel - Value = -64 - Target = Patch Volume
Moving the Mod Wheel will now change all volumes at the same time
My though: Bad idea cause you will lose the Mod Wheel as a manipulator for sweeps etc. and if you have a desktop version, like me, you do not have a Mod Wheel (or the one of your keyboard is occupied then).
My tip: Use a controller for exactly the same.
Two options:
1. Use the source of "Controller 3, 9, 12-16" and address the values above (you might like to use +63 as value)
-- Controller 3,9, and 12-16 are equal to CC 03, 09, .... so careful what the selected controller is doing to the whole matrix or the keyboard used
-- I have a PolyBrute, where the ribbon controller is fixed to CC09. This would be no good for me, as I like to have the ribbon controller doing nothing else but manipulating the settings of the PB.
2. A simple controller, where you can set the CCs to your taste would be the other solution
-- and you can spare Slot 6 for other manipulation of the Virus by setting all parts to the same midi channel, and target CC07 (Volume) of the Virus in the controller
As there are really good options for manipulation hidden in submenus, I would go for a bigger controller.
Some examples
- Panorama Spread give a great roomy spread, turning it down will concentrate all in the middle
- Split or Serial Filter spread - I love this, Filter 1 one side Filter 2 the other (great in combination with Panorama Spread)
- Cutoff Filter Link allows the manipulation of each Filter - Try it out for each setup, as it might result in loss of punch
- Note Hold is great for atmosphere type of sounds. Klaus Schulze did not have Note Hold, he used chess figures of metal 
To your last question:
- I am still using an old Yamaha RS7000 - it has additional to the 16 volume controls (CC07) for each voice a master volume knob
- Same for the MPCX
- The PolyBrute works differently - it has two independent parts but running through one set of effects. It is possible to layer them, but you will have the same effects applied. But as said - it is a completely different synth with a huge matrix.
Sorry for the many words 
Edit: Another plus for an external controller - you do not need to program the matrix every time, as it will target always CC07