That is exactly why I don't bother using media player, or itunes, or any piece of software that expects to organise my 'library' of music. I stick my music in a folder structure that makes sense to me, and use winamp to play what I want to listen to. I find it much easier and I feel like I have total control. I really don't like the library structures that other programs use.
I pretty much do the same thing
I have three main folders:
orchestral - classical - baroque - martial
swing - big band - jive - vintage - etc
rock - pop - electro - everything else
And within each of those (well, within the swing and rock folders, because I don't have much classical at all) I have a [miscellaneous] folder and then 26 folders, A through Z. The misc. folder is for compilations and random stuff, and in the lettered folders I have folders for individual artists (unless I have only one track by a particular artist, then I don't bother creating a folder for it, it just resides in the lettered folder.
I use Windows Media Player usually, for listening purposes. I'll just go through my folders and drag what I want to hear into the player. But If I want to drag large amounts, like several thousand, into that player and listen to it on shuffle, it takes forever for it to get ready to play, so for that I use iTunes, which is much quicker. I don't use any of the library functions of any media player.
A handy application to have is called Mp3tag. It's free, and it's an mp3 tag editing program, where you can edit all the parameters that media players organize song files by. I really hate how media players (and portable mp3 players) force you to organize your files. I just want to be able to use my system of file folders, I don't want stupid arbitrary classifications and ratings etc.