Craft refueling just happens when the craft is at base - every 30 minutes, on x:30 and x:00 on the clock, the amount defined in the ruleset is added to the craft's fuel reserves.
As for the suggestion of mid-air refueling, I personally think that it's something that should just be left as abstract - the standard interceptor has a range much farther than any modern fighter should, and one way of rationalizing that is to just assume refueling happens as necessary to keep the craft in the air, and the fuel is when the craft needs regular maintenance to keep flying. Adding player input to mid-air refueling sounds like more tedium than it's worth when you can just increase the craft's range passively in a mod, or by adding a craft "weapon" that adds extra fuel to the craft's range.
