When you rip with iTunes, the ripped stuff will land in the Music folder, organized by performer and album - there's nothing you can do about it, and actually it does have to land somewhere, so the music folder is as good as it gets. But if you have to rip 2000 CD's, well, just do it, rip them with the settings as above, move them away on a secondary disk from time to time and delete them periodically from the music folder. Organize that secondary HD as you like (mine is organized in a folder called music, which holds the following genres: WORLD, NEW AGE, JAZZ, POP-ROCK; in world I have the 5 continents, in pop rock I have pop and rock, in jazz I have instrumental, vocal, general and smooth jazz). Once you've done ripping, you move the folders from the itunes music folder to these folders according to your criteria; once you've done, you delete the whole iTunes library and then drag the organized music folder to the library again, in order to set the paths to the songs right. It will take some time. iTunes stores the library in XML format, and with lots of albums - in my case - it's a bit on the slow side, but I don't care.
Try it out with 10 differrent albums. If it works with 10 the way you like it, it will work with 2'000 too. Depending on your CD's, you might have to add a compilations folder to all the above.