Once you sync aircraft to the MACC they get whatever orders the MACC has for sending aircraft around. That would be depending on what mission types you gave the MACC to load in for the BLUFOR/OPFOR OPCOM to populate. So they can be doing CAS, CAP, SEAD, Recce, etc... Just because the ATC is recognized as an HQ does not mean that the airfield was indexed with the correct settings to recognize the hangars as places to place aircraft.
In that case you will need to go in and place invisible markers for the aircraft to be placed. OR place them into the mission before you upload it. If you don't want aircraft rolling away you can pull the fuel out of them or placed them into the mission without crews in them and they will not fly away.