My Spotlight days were painful. I could never get Spotlight to find things the way I wanted. Until now. I recently ran across the free SpotlightIndexer utility. I used this nifty little program to index my entire hard drive, including all hidden directories.
My searching days are now here to be enjoyed with Spotlight.
Mac OS X Hints
http://hints.macworld.com/article.php?story=2006021723064954