Some of the aircraft in Aces High II can have multiple fuel tanks. 

For example, the P-51D has three internal tanks, they are labeled LW for left wing, RW for right wing and AUX is the tank in the fuselage.  If you load drop tanks, you get 2 more tanks labeled extern. 

At the start of flight you will see an A- in front of the tank name.  The A indicates that you are in Auto mode and the program will select your fuel tanks for you.  It does this by 2 simple rules.
1. Always select external tanks first.
2. Select the tank which will keep your CG (center of gravity) balanced.

When you choose a fuel load it doesn't put 25% or 50% in every tank but loads them with a preset configuration.  That's why unless you load 100%, you don't see the AUX in the P-51D.

Pressing Shift-F the first time will take you out of auto mode.  Note the fuel dial only shows a % in a tank, not your total fuel.

Pressing Shift-F a second time will select the next non-empty tank.  In the case of an aircraft with only one internal tank and assuming you don't have drop tanks loaded, Shift-F will just be going back and forth from A-MAIN to MAIN since those are the only two modes possible with one tank.