As with other OGL games, judging the CR of unusual creatures with class levels (whether in a PC, NPC or Villain class) is as much art as science.

I'd use the basic outline provided by the SRD.

bAssociated Class Levels[/b]

Class levels that increase a monster’s existing strengths are known as associated class levels. Each associated class level a monster has increases its CR by 1.

Associated classes for a creature that relies on its fighting ability:

Any IH PC class except Thief or Arcanist

Champion

Demon Knight

Demonic Brute

Warleader

Associated classes for a creature that relies on stealth to surprise its foes, or on skill use to give itself an advantage:

Archer

Demonic Minion

Executioner

Hunter

Thief

Associated classes for creatures that rely mainly on magical ability:

Arcanist

Dreaded Sorcer

bNonassociated Class Levels[/b]

If you add a class level that doesn’t directly play to a creature’s strength the class level is considered nonassociated, and things get a little more complicated. Adding a nonassociated class level to a monster increases its CR by 1/2 per level until one of its nonassociated class levels equals its original Hit Dice. At that point, each additional level of the same class or a similar one is considered associated and increases the monster’s CR by 1.

Levels in NPC classes are always treated as nonassociated, and levels in Commoner count as half a nonassociated level (i.e. they only add 1/4 CR each)