I would love to do the one library mindset, but here's where I run into problems: if, lets say, after a year I go and create a new smartlist or playlist and forget that I had flac and mp3 versions of songs, I end up with both types in my playlists. Hence, redundant songs. I catch these kinds of errors ONLY when I have time so sit and peruse my library looking for tagging mistakes, spelling errors, etc. I guess I just need to pay attention as I go.
I LOVE the panes and want that to work, because strange things are happening when I try to create and/or import libraries. Sometimes this action completely wipes out all previous libraries in MC and adds the one, and sometimes it just adds as a new library in the existing list. Also, sometimes my original issue happens--where I can't delete a folder of flac, lets say, because it deletes it from every library in my system! Both of these events have happened twice, so I feel like it's not a fluke. It is really weird, but I don't have the patience to set up a test scenario and figure it out. I just set up a new windows box and I want to leave it lean and mean and not play with it too much:)