Not a Bose fan, 2X the $ for 50% of the product. Look at Onkyo 626 and an Energy Take 5 speaker system, I have this in my family room and it rocks. The Take 5 is an awesome speaker system. Unlike Bose, they don't spend a gazillion on advertising each year.

Assuming that you have a hdmi capable receiver.
The speakers should be tied to the receiver. The hdmi output of the Apple TV should go to the receiver first. The tv should in turn be connected to the receiver.

Seems like you could add an ipod dock and plug it into the aux input jacks on the receiver too. Should work for any receiver.

I agree on the Bose. Many of their products don't deliver much bang for the buck despite their advertising.

"Not a Bose fan, 2X the $ for 50% of the product."

This. Bose makes a decent product, but markets the heck out of it. There are certain limits on what you can do with a speaker of a certain size, and Bose likes to pretend there aren't.

10-15 yr ago bose made great stuff. now they ride on their name to sell.
complete audio systems run from crap to wonderful. but just the decent ones are priced high.
personally, i run a yahmaha 5.1 a/v receiver and klipsch speakers. lots of bang for the buck.
i'd suggest going on line to crutchfield.com. huge selection of components and a/v furniture.