No offence at all - you're absolutely right, it's important it's clear.
So, basically there are a few options to get home cinema sound and music from the multimedia PC. For home cinema purposes, the best thing to do is to get a soundcard in the PC which has HDMI out. This should allow you to then output the HD audio formats digitally to an AV receiver where they can be decoded (assuming the software will do this, but that's another story!).
For music, you have a few options. Depending on which AV receiver you have will depend on the quality of the DAC built into it. If it's a decent one, you can stick with the HDMI connection and feed your music digitally through to the AV receiver, which will then perform the digital to analogue conversion and then send the music to the speakers. However, you may also have a decent DAC built into the soundcard so you could instead run another cable from the soundcard from one of the analogue outputs (such as the 3.5mm output or the RCA phono output if it has one) into the AV receiver. In this case, the digital to analogue conversion is being done within the soundcard. In this instance, you would therefore need to change a setting within the software to tell it, when you're watching movies, send sound out the HDMI and when you're listening to music, send sound out the 3.5mm output etc.
You could also try an external DAC instead (these range in price from hundreds to tens of thousands of pounds). Here, you would output the signal digitally (usually via digital optical or coaxial, but also perhaps from USB) into the external DAC. This will then perform the digital to analogue conversion and is then connected into the AV receiver via an analogue connection (usually standard phono connections). Again, a change in setting between movie watching and music listening would be required.
However, as discussed, AV receivers aren't renowned for their musical ability. The more you pay, generally, the better the musicality of the amp, but this will depend on a lot of factors. As a general rule, an AV receiver is considered to be roughly the equivalent of a stereo amp a third of the price in terms of musicality. So, instead of an AV receiver, you could opt to connect the PC to a stereo amp (though obviously you won't get the ability to play 5.1 for movie soundtracks, only stereo). Since most stereo amps don't have a built in DAC, we will assume this here. In this case therefore, you can either hook the PC directly to the stereo amp using an analogue connection (which will thus use the DAC built into the soundcard) or you could connect into an external DAC via one of the digital connections in an attempt to improve the sound.
Finally, there is another option which links the two, whereby you have both an AV receiver which includes front pre-outs, and a stereo amp and this should give you the best of both worlds i.e. the benefit of using a stereo amp for music, whilst also getting 5.1 sound through the AV receiver for movies. To be honest, I'm going to leave it here as I don't want this post to get too complicated, but if you're interested, let us know and we can go through this as well.
Hopefully this has cleared up any misunderstandings - basically, there's no right or wrong in any of the above setups as all the components being used determine how it will sound and therefore which is the right way to hook it up. It's only when you know what those components are that you can start looking at it and saying whether one thing will obviously improve the setup, or whether some testing / auditioning is required to see which connection is preferred.