aa is short for "anti-air." In other words, the command must be performed against an airborne opponent.
So for example, if you block Scorpion's teleport punch and then hit him with a high punch, you are performing an "aaHP."
So combos that begin with an "aa" notation can be performed on a jumping opponent, or after blocking a move that puts an opponent into punishment mode, etc... various situations in which the opponent is vulnerable in the air. If you see aa in the middle of a combo, it means that the following hit is juggling the opponent in the air.
