False positives are both a good and a bad thing. Good in that it tells you your scanner is at least trying to protect you. Bad in that its like the boy who cried wolf. Eventually you get numb to the warnings and something will slip past. Your best friend in all this is Google. When you get an alert, Google it. Find out where the suspect file is supposed to be at and compare it with the one on your computer. If its not were its supposed to be, odds are its being naughty and needs a spanking. If it's in the right place but you think its kinda fishy, go to Virustotal and have it analyzed. Its a quick free scan that runs thru 30 different malware checkers.
Get in the hang of Googling the running processes on your computer. Learn what each one does. The more you know about your computer, the quicker you can detect when something isn't right and take action before it really becomes a problem. There is a caveat to that though. Don't become paranoid like I first did when I started Googling random system files. Make sure you read more than just the first couple of google entries, otherwise you might find yourself deleting core system files and really causing havok.