You can flank with a reach weapon. Flanking has only three requirements:
1) you are making a melee attack
2) the opponent you are Flanking is being threatened by an ally
3) said ally is in a position opposite the opponent from you (see definition of opposite below)
When making a melee attack, you get a +2 flanking bonus if your opponent is threatened by a character or creature friendly to you on the opponent’s opposite border or opposite corner.
When in doubt about whether two friendly characters flank an opponent in the middle, trace an imaginary line between the two friendly characters’ centers. If the line passes through opposite borders of the opponent’s space (including corners of those borders), then the opponent is flanked.
Exception: If a flanker takes up more than 1 square, it gets the flanking bonus if any square it occupies counts for flanking.
Only a creature or character that threatens the defender can help an attacker get a flanking bonus.
Creatures with a reach of 0 feet can’t flank an opponent.
I copy/pasted it from the 3.5 SRD (because I'm lazy), the language is nearly identical to that in Conan AE. The difference is Conan AE adds a clarifying note concerning dodge and parry but the important bits are the same.