It shouldn't be a problem. Make sure Takeoff time is IMMEDIATE. In the Mission Builder, don't worry about who is set to HUMAN and who isn't. By default, the first aircraft placed gets assigned GROUP A, and will be HUMAN (I think). As long as the flight has a Briefing Group assigned to it, the HOST in a Multiplayer game can assign pilots to it.
Try it in Psuedo-Multiplay and see what happens (i.e. start a multiplayer game as host, and just fly without connecting to anyone.) You should be able to assign pilots (yourself) to any Briefing group).
When flying non F/A-18E in Single or Multi, make sure you go to the arming screen to add ordnance. Funny things happen if you try to leave the default load as set by the mission builder....like the aircraft being SEVERELY overweight.