I'm a comp sci major (or the equivalent in the UK), I did have a little experience with Linux, I thought that I'd be okay in a couple of days too. I'm a year and a half down the line with two dedicated boxes and though I can set things up okay, I wouldn't have the faintest idea what to do if something went wrong (and I have to get someone in when I there's something even remotely non-standard happening). I have nightmares about it sometimes and I'm moving onto something managed asap. It's just not worth the risk.
If your site is generating enough traffic to require a dedicated server then it's probably earning enough to warrant paying for a managed box, or to pay someone to manage it for you. My personal advice: stick with this route.
If you've got the time to spare (I haven't and this is the problem) then get a cheap dedicated box and spend time playing with it - don't put any 'real' sites on it. Make sure you can install, upgrade and secure every single piece of software that you're using. Once you're comfortable start moving things on there.