Tork:
Auto mode pretty much takes over your plane and you can walk away from your keyboard. It keeps your plane either in a climb or level flight, or even in a controlled dive. With the governor on though, you cannot do anything manually unless you take over the controls again by using your stick to change direction etc.
I use auto for climb outs and level flight when I have a long way to go and want to get a sandwich. When you want to actually do something you need hands on control. The trim functions enable you to climb, dive, turn etc. in a smoother manner thereby losing less E. You should spend a lot of time offline and online learning them and getting used to them. They help a lot in combat situations when you want to climb up and away swiftly, or dive out and away in a hurry.
