Confused about Encoding Sound in Video Files...

I have to admit I am totally new at all this video conversion on building an iTunes Video library. The idea is to build a library of some of the stuff I own and a few Tv series. I am using mainly MP4 Tools, Handbrake, and MetaZ to convert and tag the files.

My main problem I come across is that I am playing the files on my mac via an ATV3, hooked up to a 2 channel Onkyo receiver. I have an optical output on my TV that I connect to the Onkyo Receiver. I have no way to really have a surround setup, and the stereo works great for me.

But what often happens is that I will convert a file and the video will play, but I will get no sound. Through trial and error I figured out that if I convert to AAC 2 channel it will play. But it also strips the other channels.

So I am looking on advice on how I should be converting these files. Can I have multiple audio tracks in a file and still have iTunes play it like VLC will do?

Can't find a way to pick audio tracks in iTunes, or am I stuck converting all these file just for the ATV and my stereo setup?

I'd like to only convert these files once, but having trouble at what file formats and audio tracks to use that will be semi universal. I am not even close to figuring the close captions out.

Any advice for someone setting their video library up? or a link to a good FAQ or tutorial?

It seems like such a big task, I never get started on it.