One possibility, which has been used in NASCAR games, is to set what will occur in the pitstop before the pitstop is actually performed.
in Sierra's NASCAR game, You would adjust tire pressure, downforce, select which tires to replace, and how much fuel to add. You would do this while you are racing (the straights in nascar give you some time to do this

). Then, when you went into the pits, the proper changes would be made.
A simplified way to do this would be to have a quick pop-up selection come up as soon as the auto-drive in the pits takes over. Just a small overlay selection menu window, and as the auto-drive takes you to the pits, you have a few seconds to choose from FUEL ONLY, TIRES ONLY, or FUEL & TIRES.