Ive got a set of woodland and three color desert raid mod'd.
Mine have no pockets (other then the little pen pouch) left on the front. The upper pockets moved to the arms on an angle with buttons left in place. 4" velcro ID on the pockets , pretty simple mod.
I have seen the lower pockets moved to the chest and slanted inward. I have also see some instances where the lower pockets were put on the calf of the pants and very rare occasions actually moved and slanted outward to the kidney area. The latter being more useful for dm's , snipers , cct's and others who spend more time prone.
Its a kit mod so really there isnt a "wrong way" mod the bdu's based on your role and your current equipment.
Check out MM's raid mod'd bdu's.
http://www.militarymorons.com/gear/gear.1.html