Let's say I have a Dark Naga, who casts as a 7th-level Sorcerer from its racial hit dice. Then I put the simple class template for a Sorcerer on it. Normally, a 10 HD creature would cast up to 3rd level sorcerer spells with this template and gain +2 CR. But how does this interact with the creature's inherent spellcasting abilities? Should I just give it Sorcerer class levels and accept the +1 CR per level from matching the monster's Spell role?
I don't think it's intended to get the template or the levels. If you want to stick with either, probably treat it as a separate pool of spells - like multiclassing a wizard and a sorcerer. But keep in mind the naga is still bound to one standard action per round.
I'd prefer the following options:
* Apply two templates to get +2 CR. Advanced and fiendish come to my mind first, but giant and resolute might work also.
* Increase hit die by 3 and caster level by 2. Add some 4th level spells which fit thematically (illusion and damage spells). Let it cast 1st level spells unlimited times per day. You could use the Guardian Naga as reference (beside its spell selection).
* Use two of them, being twin sisters or something more exotic (a clone, a living mirror image etc.).