For example, Snake...

gets +2 to several (healing, detection... I dunno, too lazy to look 'em up =[ )
and gets -1 to all spells cast in combat.

Is that a net +1 to whatever Snake gets bonuses to and -1 to all others, or -1 to everything?

(that is, when a spell falls under both modifiers, do you take the net or just the negative?)

As far as I'm concerned, you take the net, taking everything into consideration.

If Sidewinder the Snake Shaman was casting Treat while in combat, he would get +1 dice to use.

net. there's no ruling that i know of either way, and net makes the most sense to me.

I'll add both Adv. and Disadv. together.

So it is net as far as I'm concerned