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I too had my ebooks in their own directory before I found Calibre. I also manually managed my music files as well. I have come to realize the benefits of letting Calibre manage the files. Let me give you an example.
This summer I had a huge hard drive crash (it died completely) and had to reinstall everything. My Calibre library was backed up with Dropbox---I had gone into Calibre, told it to create a directory inside my dropbox folder and then all the files, it put there. When I reinstalled the dropbox folder on my new hard drive, all I had to do was download Calibre again, tell it 'all the books are there' and bingo, everything was back as it was.
Contrast this to iTunes, which I had been manually managing. I thought Time Machine was backing everything up, but Time Machine only backs things up if you keep them where it thinks you are keeping them. By managing it myself, I found I could get back my music files, but ALL the metadata was lost. So when I put everything on the new computer, I took the same approach with iTunes as I did with the ebooks and let iTunes manage its own files, within the directory of my dropbox folder that I specified (i.e. I told it to yes, make its own directory and manage its own files, but do so in XYZ location). Now, I don't have to worry about what will happen if my hard drive goes again. I can just re-install iTunes like I did for Calibre and tell it where to find the files.
I also found, as my ebook collection grew in size and complexity, that some books applied to more than one category, so the tag-based system was easier. For example, I read books in French for fun but was also at one point taking a course in French for which I also had to read books. A tag-based system allowed me to have a book with both tags, so that a search for all French books returned it, and a search for only books for the course returned it also.
It was a change in mindset at first to get out of the folders and trust Calibre to manage everything, but it turned out to be for the best.
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