I've been playing hunters since alpha of wow over 4 years ago, and lvl'ing them, I never really saw a big need to use all my big shots.
Big shots mean aggro to you, and you don't get MD till late, although you should be getting FD if you don't have it allready.
Personally, I send all my pets in, auto, then throw up SS with all 5 toons.
It's the same prinsciple as locks/sp, and any other caster class that uses dots to kill a mob, focus single target dps. One pet managing aggro, while the other's pick up the extra dps.
Are you using growl on one or all?