Simple question, are you flanking if you are inside an enemy's space? Say you're a Medium creature underneath a Huge or larger creature with an ally adjacent?
Nope.
When making a melee attack, you get a +2 flanking bonus if your opponent is threatened by another enemy character or creature on its opposite border or opposite corner.
When in doubt about whether two characters flank an opponent in the middle, trace an imaginary line between the two attackers' centers. If the line passes through opposite borders of the opponent's space (including corners of those borders), then the opponent is flanked.
