Library specific iTunes preferences?
iTunes preferences are stored in

~/Library/Preferences/com.apple.iTunes.plist


I presume you access your two libraries by launching iTunes while holding down the Opt key.

An alternate method to launch iTunes and swap out pref files at the same time would be to make an Automator or AppleScript app that switches pref files, and makes a link from ~/Music/iTunes to one of the libraries, then launches iTunes for you.