I used to have them separated but a while ago I just mixed them all in. It was too confusing to keep shifting them around when I added one, since I keep everything alphabetized.
I keep everything together and have them in my cases by release date. If I purchase something released a couple of years ago, I just shift. If I am possibly interested in something released several years ago, I just don't purchase it. It's easier to do, than to shift a ton of cds. I have over 3,000 cds, but one would never guess that. I keep them in cases that are made for holding 1,000 cds. It is very compact and contemporary looking.