Course plotted, sir!
This shows the map zoomed in on your ship, base, mission target, and plotted course destination during a training bombing mission.
The game includes an autopilot AI feature that will automatically fly the ship to any destination you choose from the world map in the chart room.
Maintaining altitude, however, is up to you. There is no "elevator officer" AI (as of yet). But this really isn't a problem. The weather engine isn't in yet, so all you have to do is reach static equilibrium at some appropriate altitude, then plot course, kick up the simulation speed (the simulator supports accelerated time), and wait to arrive.