I am running a remote mysql server and thus I don't require mysql running on my apache server. I am using WHM/cPanel, and for some reason mysql just pops up in my services list, after I shut it down, it's fine until a few hours later when it turns it self back on or something.
Any idea how I can tell mysql to not start at all on my apache server?
You may well still need your local MySQL instance for local applications that use databases to store settings/logs/etc.
A basic MySQL install with a small database that is being accessed only occasionally (such as the back-end database of your Cpanel install) should only take up very minimal resources and will hardly be likely to impact on your Apache server at all.
Have you checked the resources your local MySQL install is actually using?