Checkboxes are universal, meaning that unchecking them in the library but checking them in a playlist can't happen. A song's box will all be checked or unchecked at a given time. However, this does let you make the act of checking/unchecking simple.
If you have a Christmas playlist, or some sort of grouping in iTunes that has all the music you don't care about them, browse to that playlist, select all the tracks (cmda, right-click -> select all, however you wish to go about it), and then right click one of the tracks and click 'Uncheck Selection'.
Massive amounts of tracks instantly unchecked and will not be considered for Genius, iTunes DJ, syncing, anything.