Not sure if this is webmaster or a WordPress question, it's a bit half and half, sorry if I'm posting in the wrong place.

Without using Multi-Site or installing new WordPress CMS' in second-level domains, what's the best way to get multiple WordPress installs running on my VPS (running Linux powered CentOS 6 with WHM and cPanel)?

It's currently working but only by setting the permalinks option to the default setting, so the URLs aren't human-friendly. I have come across something called WPSiteStack, though I'd really rather not go down this route.

Long story short, I need the following:

• Seperate installs so one core / theme / plugin update doesn't affect all sites and increases security of all sites;
• 'Pretty' permalinks;
• Each WordPress install must be in the root of it's own domain to ensure that I can accurately measure my clients' quotas;

It may also be worth noting that some functions within each install use the $_SERVER['DOCUMENT_ROOT'] and $_SERVER['HOST'] variables.

I have already edited the httpd-vhosts.conf, httpd.conf and .htaccess files but this hasn't made any changes.

So any ideas what I'm missing or doing wrong? Any help is much appreciated.