The way I've seen it, you still only have one favored class, so you'd have to decide at character creation which is your favored as normal, and then pick up your benefit whenever you gain a level in that class-- and it would be class specific, so feel free to multiclass away with your other set of levels.
This might make the Half-Elf kind of borked, since Multitalented turns into Free Toughness at the least. The 3.5 gestalt guidelines don't mentioned favored class bonuses though, so talk to your GM before anything else.
