I don't know what you're using for software, but I just use the standard blizzard interface, and I have one issue with multi-boxing a hunter as a NON main. After ever combat, before moving I have to hit the follow button, as his ranged attacks seem to break follow, probably due to auto shot. My other casters never have that issue. I think Jamba or something would likely make that a non issue, but I don't use it. (I use HKN, Tom Tom, & Recount Lite, and nothing else!)

And with the Hunter, macro EVERYTHING!! Otherwise, he'll find some way to shoot something that you didn't intend, or send his pet to pull everything in sight! That's not really a problem questing, as your goup will be so powerful they can deal with anything that agro's, but in instances, it can be deadly.