As I understand at present CIVA system in VC is only a pure visual joy.
That's the way it is, yes. You can show some coordinates (not the Civa processed ones, but the ones from FSX itself) and the alert signs there though. So it's partially operative if you'd like to say so.

Yet I am curious how many CIVA systems are present in VC after panel.cfg file modification? I suppose both Bendix doppler navigation systems should be replaced by two CIVAs.
That's where the tricky part comes in.

Without tweaking the Civa gauges itself (which would require knowledge and approval of course), you can place them in the VC but they will be flat and the 3D model of the airplane (which most likely isn't flat at all) then makes them look "strange" (can't describe it any better, one has to see this for himself).

The other and much more important limitation then would be that every unit can only be shown once at a time.
So while you could place some Civa CDUs in the VC, they can't be present as 2D popups too.
CDU 1 can only be shown once, so does CDU 2. Placing them both in the VC and opening up a 2D popup (for the ease of operating them) will fail and most likely make the VC ones look odd and useless.
There's some plane on the market using the Civas in the VC and on a 2D popup at the same time, but this one plane has unique Civa gauges, tweaked and protected, so we can't compare them to our freeware source here.

I've covered these limitations in another thread before, so see this as the brief version.  :)