A bit confused.

[salmo]

G'day Mike,
Full Mission Builder: You could start by looking at some FMB video tutorials HERE. They're for IL2-1946 but most of the information is transferable to COD. There's also a beginners guide/mission HERE.

How do I set the AI to spawn parked and take off to meet the player aircraft ? To spawn aircraft with the passthrough trigger. (1) create the AI flight you want to spawn. Make sure the 'spawn on script' checkbox in the group's properties tab is ticked & it's also set to 'spawn parked' (2) create your passthrough trigger, on the trigger's action tab, select the Ai flight as the trigger target.

How do I allow players to assume gunner and bombardier positions in a player controlled aircraft? Players can jump into any position in an aircraft but there's a bit of of a trick (because of a game bug). Online - When you enter the mission you will see a list of planes. You can usually take a pilot position, but other positions will show as an 'unavailable puppet'. For other positions, from the main menu you need first select a plane, and spawn in that plane, then back out to the main menu again then all available positions in the other planes will be vacant. Click on a vacant slot to enter that position.

c# Scripting:
Kodiak has information on how to setup for C# scripting and a simple scripting lesson HERE.

How do I set mission goals and attach those goals to land (or air) based targets? - You'll have to script this when you're comfortable with basic scripting. Use the OnActorDestroyed event to test whether your targets have been destroyed and code what you want the mission to do next.