I might be misunderstanding the question, but CC conflicts can be an issue sometimes when working with remote maps in a DAW. There may be several methods to address this, but this is a personal approach that has saved me much trouble-shooting and grief over the years.
First note that Halion can have the QC set driven directly by MIDI CC events in a MIDI part, or on MIDI Instrument track 'controller lanes',
or you can directly control them via VST protocols on the VST plugin controller lanes.
This can be a bit confusing to say the least...as one method is stored right there in a MIDI part, or on controller lanes that live on a MIDI or Instrument track, while the other is done in controller lanes on the VSTi track itself (The track that shows Halion is loaded, and lists its assigned output ports and VST controller lanes). One can snap the QC set to H5, and such automations will show up down in the Halion VST track, but you'll also notice there are many pages of choices, as well as a method to go into the plugin's VST assignments and remap them to your heart's content.
If you want to automate H5 via VST, it's an extremely powerful way to do it. You can get to almost every little parameter in the Halion Engine that way. The scope of these possibilities is far too broad to try to cover here in this thread, but the potential does exist! This sort of automation is done in the VST track for Halion 5 itself, and Quick Controls can be assigned to them on an as need basis.
Personally, I keep it simple most of the time, and drive Halion 5 parameters using MIDI CC events right inside the MIDI Part on controller lanes, and more or less ignore the QC stuff when working with Halion 5. I've built an H5 preset on my MPK2 with this stuff mapped out so I can record right into MIDI tracks for H5 live, and not be bothered with linking QC.
Page 171 of the Halion 5 manual wrote:
#91 Effect 1 Depth
#92 Effect 2 Depth
#93 Effect 3 Depth
#94 Effect 4 Depth
#74 Program QC 1
#71 Program QC 2
#73 Program QC 3
#72 Program QC 4
#75 Program QC 5
#76 Program QC 6
#77 Program QC 7
#78 Program QC 8
If you're like me, then you'll probably want to use your QC set for way more things than moving a few knobs in Halion. So, make sure your Quick Controls (QC) map is using a device and/or CC messages that are not conflicting with your other remote maps, or with a loaded VSTi. You can get to this map in the Cubase "Devices/Device Setup" menu.
Notice you can choose what MIDI port Cubase will listen for these QC events.
One way to sort out CC conflicts is to take advantage of multiple ports if your controller offers them.
My Akai MPK2 has two ports over USB (an A and a B, as well as some other drivers that can be used to access the DIN ports on the MPK2). When ever I want to send messages through an armed DAW track to a VSTi or external Synth, I'll make sure my MPK2 controller is sending its CC messages over the A port. In turn I'll make sure the MIDI track(s) that need added isolation are set to get user input specifically from my MPK2 port A (rather than ALL MIDI Inputs).
When I want to work with Cubase Remote and Quick Control Maps, I have the MPK2 send CC messages over the B port. I've got to be sure that I don't have different maps listening for the same CC events over the same device/port/channel at the same time, or they could conflict and be a nightmare to trouble shoot and sort out. So I personally keep a spread-sheet handy and jot down CC events that are in use...and empty ones are fair game for new assignments
Another method is to simply make sure your QC maps are using CC messages/channels that nothing else uses. If your controller does NOT have multiple MIDI ports accessible for creating a bit of isolation, then reserve and have your QC map use a range of CC events and/or channels that your VSTi/Synths do not use. In the case of only having a single port to work with, in my experience, confusion and conflicts can be avoided if I first disarm tracks from 'recording/monitoring' when using a QC, and instead write the data to a track 'controller lane' (Read lights up green, and write lights up red, when red is lit up one can make adjustments while the DAW is playing).
For me, 'isolation' via MIDI port comes in handy for my big Cubase 'generic remote maps' as well. I keep all Cubase remote control events on a different MIDI port from anything intended to control a VSTi or external synth directly. 'Generic Remote Maps' can be as large as you like, and can be used to trigger pretty much any Cubase command/option via remote MIDI events. You can even activate and use multiple Generic Maps all at the same time. Again, it's quite useful to keep MIDI events intended to drive Cubase directly isolated and separate from events that are intended to control a VSTi/Synth directly. This is why many (if not most) keyboard and MPC controllers out there give you more than one 'MIDI port' to work with.
Once you've got your QC map set up in 'isolation' it becomes easy to snap any of your quick controls to any track lane you like. You can do this through the "Quick Controls" tab in the "Track Inspector". From here you'd simply toggle the track's QC set on and off as needed.
You can import the VST's standard setup, or you can build your own for each of your 8 assigned QC CC events. You're not limited to H5 stuff either...you could also have a QC control the aux send, or something in an FX plugin, and the list goes on.
In short...keeping your QC and Generic Remote maps as 'isolated' and unique as possible will help avoid creating a CC conflict by mistake. Your 8 Quick controls are there for easily snapping the same set of sliders/knobs, or whatever to anything you like in Cubase.