I find Spotlight does miss some files for some reason. The Preference folders are in your User Library normally. (Home>Library>Preferences)
I found it weird at first not having an uninstall option on applications etc but Ive discovered that if you just search in every folder on your system and get yourself used to where certain things go/end up you start to know the system better. Lets face it... PC OS's are so pointlessly massive, and OS X is compact and set out so you can find stuff easier. 😀