It is my understanding that when "A" appears before the fuel tank designation the fuel is automatically drained from various tanks at and will try and maintain the best Centre of Gravity for the aircraft.
Pressing "Shift-F" will manually switch tanks and if no "a" is displayed then only the tank selected will be drained (with resulting CoG effects).
I often fly with a drop tank and only consume fuel from the tank initially. Then when I approach combat I switch to automatic fuel consumption and drop the external tank. I may or may not have more that 100% in the main auxiliary and wing tanks, depending on the sortie. Dropping the tank before switching the fuel source results in fuel starvation and a momentary panic as the engine quits.

Cheers,
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phaetnAT
Aces High Alpha Tester
(trying to respond as best he can).
[This message has been edited by phaetn (edited 09-29-1999).]