There's a couple of ways to do it, depending on how 'realistic' you want your refueling to be.  One is you find the yellow squares at almost any airport and pull your aircraft into the center and come to a complete stop.  The tanks will top off automatically and you can be on your way.

The second way to do it is available at any time.  Just press ALT any time during the flight.  This will make the pulldown menus at the top of the screen appear.  Go to AIRCRAFT and then FUEL.  This will bring up the main fueling screen, like the one in the selection menu at startup.  Its pretty self-explanatory, just enter the amount of fuel you want and press OK.  Voila!