You are basically correct.
Most people use zones to allow the playing of music to different rooms (zones). So if you have say 3 outputs from your htpc you can have each run as a seperate zone. You may have an HDMI output as one zone, the motherboard line out as another zone and maybe a spdif or another analog output on an audio card as another zone.
I used to have an M-audio delta 1010LT running into a multi channel amp to drive my kitchen, bedroom, and outdoor speakers. The amp sat under the PC and I ran speaker cables to every room, this may not be a great option for you though.
You can also use DLNA renderers (like the JRiver ID, which is wireless) to provide the audio signal to an AMP to run Zones in other rooms, or use a PC as a library server client, which means it will share the library with the main htpc and can be controlled locally or from the server.
Once you have your zones configured, they all appear under "Playing Now" So you just select the zone you want and then browse and play your music like normal. You can also "link" zones together to play the same music to multiple zones at the same time, with some basic options to try to get them in sync.
Hope this helps.
Richard