What is the difference between the /Library/ directory and the /System/Library/ directory? I have, for example, a perl/ directory in both places. If I'm installing a new perl module, which location should I put it in?
the /Library/ directory is for your systemwide stuff. /System/Library/ is for Apple's systemwide stuff. /System/ should not be modified by anybody or anything other than an Apple installer.
So put the module in /Libary/ if you want all users to have access to it, in ~/Library/ if you want only you to have access to it.