OK, here's a setup you could use:

Let's say you log into your server, via SSH, or FTP, or what have you. Then you will be in a "top directory", let's call it/server/, OK?

(Often, this will be something like /www/, /webroot/, /httpsomething/, etc.)

The important thing to note here is that none of our domains or subdomains will point to this "top directory"! Instead, we are going to create a web-facing area, called sites/, as well as an admin area for ourselves, backup, etc., let's call it admin/.

Furthermore, we will create a directory for each web-accessible sub/domain target. Then we end up with a basic structure like this:

/server/
    admin/
        … your admin stuff: tools, backups, etc.
    sites/
        yourdomain.com/
        assets.yourdomain.com/
        … etc.

Note here that for example assets.yourdomain.com/ is a directory which we have given the name of the corresponding sub/domain we want to point at it. However, this is just helpful to us, but doesn't mean that the sub/domain will somehow automatically point at this directory!

Instead, we still need to establish that link in the cPanel, or whatever provider-side tools you use to assign sub/domain targets.

Is this making sense now?

To came back your original question, here's how you might lay out your media assets:

I would create a media/ directory, containing a separate directory for each type of media asset, such as video, audio, etc. Since media assets are created on a certain date it's usually a good idea to sort them into years and/or month. Depending on how many files you have for each media type you can choose the level of granularity to optimize your year/month structure:

assets.yourdomain.com/
    media/
        audio/
            2015-03-21/
                …
        video/
            2015/
                /2015-01/
                    …