Using your example (6 total magic, 3 for adept powers, 3 for magician powers), if he's using a magic linked skill such as Sorcery, Conjuring, Banishing, Enchanting, he rolls Skill + Magician Magic (or Skill+3). However for maximum force and the like, he uses his total magic. So he can cast force 7 spells or summon force 10 spirits if he wants. Hits are capped by the force of the spell you're casting, not your magic attribute. If you're overcasting, you can keep more hits than your magic attribute.
The FAQ says the opposite of this. However the FAQ deals with SR4 and not SR4A where it worked differently.