I believe one was for professionals and the other one for students. Don't remember which one, I guess Overflow is for professionals since we use it for coding.
Honestly it’s Stack Overflow that’s really the "noob" level programming discussion, with 95% of questions incredibly elementary, whether "professional" or not. cstheory.stackexchange.com is more analogous to mathoverflow.com in that it’s about research-level questions.
I think Math Overflow was the first overflow instance after SO, so it has a sort of a special status and its own domain. *.stackexchange.com came later to meet the growing demand for more instances.
