You can use a remote control with an RF repeater, which has IR emitters to control equipment that is hidden. IR repeaters are prone to problems from sunlight, plasma TVs and florescent lights. The RF units are much more dependable. If the cable box is Scientific Atlanta, leave it on unless your cable provider has programmed them for discreet ON/OFF. Also, some have a setting that causes them to turn off if it doesn't receive a command for a certain amount of time.
You can use a Sonance, Russound, ReQuest IQ or other system for distribution. Crestron is the king but the others work well. The ReQuest has 4 zone output, can store .wav and FLAC full data files as well as MP3 for streaming on as many computers as you want, from any location that's online. I have the N1.200 server and since I have it connected to three amps, it lets me listen to the .wav audio, but after opening a port in the router, I can stream it or control it from my laptop (wireless), desktop (hardwired) or a remote location outside of the house. I have enabled IR reception, so I can use one of my universal remotes or the one that came with it, too. It has an IR jack on the back, which accepts signal from an RF extender/repeater via a cable with mini plugs. If you decide to use a controller that uses RS232, it works for that, too. It has on-screen display in different modes (NTSC/PAL, Composite, S-Video or component) and the new models have the ability to connect to a NAS, so hard drive size isn't vendor specific. You can create playlists, edit, play random/shuffle/continuous/repeat modes. The sound quality is better than any other server I have listened to.
If you want a lot of flexibility, lower price, discreet commands and decent power, consider buying a separate receiver and an Airport Express for each zone. That way, you can stream to each zone, control them from any computer, listen to various sources, 4 different radio/XM/Sirius channels and with assignable IR outputs, there's no reason to worry about one zone inadvertently controlling another.