This old topic again
The one thing to do is: trust the program to do its job, and you'll be very happy using tags to find what you need. Just keep out of the internal library, unless you have a very good reason to be there. One thing mentioned is having to share the books with other people and programs continuously; in that case Calibre would not be a good choice as it, indeed, black-boxes the directory.
I have al lot more music than I have books (around 800 albums, some of which are 10-CD box sets; one even is a 40-CD classical set), and I love to find things using tags. However, as I use a program that lets me define the directory structure it uses when importing (Foobar, which basically is the 'calibre for music' IMHO, although it only exists on Windows), I have enough OCD to actually define the folders as seen in the screenshot:
\Music\FLAC\%artist%\%year% - %album% [%genre%]\Disc %number%-%total%\%track% - %title%.%extension%
(All my music is FLAC, but I also have an MP3 folder, which houses game soundtracks provided by GOG.com. Some of the newer games actually come with FLAC soundtracks. YAY!)
Yes, I know Howard Shore is not the artist, but I don't care. Over here, Howard Shore (composer), Capercaillie (band), Karen Matheson (singer), Jimmy Smith (composer/lead artist/sidekick) and the London Orchestra are all artists. Also I only ever have one genre for music. As with my e-books, I always use the very first publication date for an album, not the publication date of the actual edition. Thus I have CD's that were published in 1957.