Plot Course is a vehicle action on page 237. It reduces the Setback dice inflicted by difficult terrain by 1 per success. Easy enough, but it says "Average Astrogation check, Hard Perception check". This differs from "Spoofing Missiles" where two skills are listed but an "or" is placed between them. Does this mean that both checks need to be made for Plot Course, or should it have an "or" too (meaning just one of the skills should be used)?

Lastly, I initially assumed that the results of Plot Course lasts for just for the next check, but it doesn't list a duration. How long should it last? I am considering 1 turn plus one turn per Advantage.

I think the "or" should be assumed, otherwise you are opening up a whole can of worms with interpreting two linked skill checks. "I got three fail and 2 advantage on astrogate, but 4 successes and 4 threat on perception..." Plus it would make the action way to hard to pull off compared to say Co-pilot. Risk vs reward and all that.

As for duration, your idea is as good as any.

The "Plot Course" action is frequently used at my table. The way I run it is that we use Perception in vehicles and Astrogation in starships. It applies to the pilot's next Piloting check; so far this has usually been the next action slot, so no issues there. Should it ever come up I'd rule that if the pilot does something other than piloting on his next action, the benefit from Plot Course is lost and the copilot must make another check.

There are many cases where you can choose between two different skill checks, and the choice is up to the player. I'd say this is such a case.

As a GM I'd certainly treat it that way. If a player has a terrific Perception and they'd rather use that, that's cool.

Yup, either/or is the way to go. This game is great in that you can easily increase or decrease a given difficulty depending on what skill is used to accomplish a given task. "Yeah, you COULD use Athletics to kick-start the hyperdrive, but Mechanics or Computers is likely to have a better result."