No operator will appear unless it's assigned to an airport. For a VA, you might probably want to choose between two solutions:
1) Assign your VA only to the airports you fly with that VA
OR
2) Assign your VA everywhere to take precedence over every operator, everywhere.
#1 is obtained by customizing the parking positions of the affected airports, and add the name of your airline to the parking codes. You can be as granular as you want, selecting either a single parking, and add your VA to the already existing atc parking code or replace them, or you can select a whole terminal, or even the whole airport, and the changes will affect many parkings at once
#2 is obtained by adding your VA name to the global GSX - Settings -> Simulation -> "Virtual Airline override".
Note that, the atc_parking_codes you insert, either in the parking customization or in the global Virtual Airline override, must match the atc_parking_codes you have set in the SIM.CFG of your repaint. That's the link between the code and the object.