Did you get a better grasp of what is going on? Your “well” implies to me that it’s working but you don’t quite know why.
I came across your post because I’m programming my VG-800 today by building upon the patches and assigns I’ve already made for my SY-1000. It is going to replace my SY-1000 on my board and I want the VG-800 to do most of the same things.
When starting out with MIDI, I recommend starting out by just transmitting MIDI from the Morningstar to the one troublesome device. This can help you narrow down issues.
To help avoid confusion when programming, I also try to dedicate one CC for a pedal, and then not use that CC again. It helps me remember what each CC does on my pedalboard. Even if a device is on another channel. This system will work until I run out of all the CCs, but that seems far away! (I attach a spreadsheet below that shows my SY-1000 has CC#1-11, and MY GM-800 has CC#12-15).
When I enter a Bank, that is when I send Program Changes. This changes the patch on each of my devices. When I press a footswitch on my Morningstar, that sends CCs to all my pedals. Each Morningstar Footswitch Press sends out a different section (or “scene”) for each song. But some footswitches near the top do other things, like take me back to my “Home” page where I navigate to songs, and one is a tap tempo that controls ableton.
Vguitarforums has deep dives into VG-800: BOSS VG-800 General Discussion
When I first programmed the SY-1000 I got a lot of headaches too. To help those in the future who come across this, here are some screenshots of my workflow for controlling BOSS Assigns:
As you can see, CC#1-11 is being sent to the SY-1000. But there are 16 assigns, where I can map a CC to control other things (like FX3 is the pitch shift effect that is controlled at the same time as string bend control is shifted).
~Please note, the ASSIGN page is slightly different than the spreadsheet (these screenshots were taken at different times, and my pedals/programming needs had shifted). But the screenshots do convey my basic system for keeping organized~
Hope this is helpful! and not just more confusing 