Well you can "tweak" MySQL by editing this file. Honestly, given your experience based on what it sounds, I'd avoid you not entering SSH.
Higher someone to do the work for you. It doesn't really sound like you have a clue what you're doing, as you didn't given us really any spec information on the server minus having 2 CPU's. You also didn't tell us anything about the sites that was running on the VPS.
Seriously, it sounds like if you start messing with things, you're going to be in for a world of trouble. Just trying to help you out, please don't take it the wrong way.