Well, go ahead and run this from the terminal:
sysctl -a
You can see how many different things you can set. The app doesn't have all that many options, if I'm not mistaken. That being said, you shouldn't change anything if you don't know what it does. Take a look at that one link above, and you'll see that some of those things are configurable from the app. It's up to you to decide if you think it's worth it, but make a backup, first. As for things in /sys, you usually change those things on purpose, or don't even realize you're changing them. That can't be done from that app, I don't think, so you'd probably only do that if you meant to. You usually use init scripts for that kind of thing.