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Atmospheric Friction is outlined in the Starship Operations Manual pg. 52.
What does it take to move between layers? Am I just missing it?
Chapter 2: Starship Combat / Starships in Atmosphere / Atmospheric Friction
There is nothing special about changing layers other than it will presumably take time (how long will probably vary by planet): You basically just need to climb or descend until you reach the layer you desire (just like a 'real world' commercial airliner initially takes a few minutes to climb to its desired 5-7 mile cruising altitude and then needs to descend when it reaches its destination).
Not quite a rules question, but I till note that every time I've seen the atmosphere rules used it has been an absolute fun spong to starship combat.. which with some groups is saying something. The solution to the pilot being the only one with any choice was not to punish the pilot for moving.