Onyx is fine, but if you don't shut the computer down after each use (just put it to sleep) it is unnessesary. Then there is the somewhat magical Repair Disk Permissions before and after installing any software or system updates. You will get a lot of "We are using special permissions for..." messages but this is normal.
Restarting, or erasing a programs preferences will often fix wackiness, but I haven't seen much of that with my machine. Enjoy your machine and come back if you have a problem. Best wishes.