Can CPU cores be separated for MySQL?
If you mean getting MySQL to engage multiple cores, you have come to the right place.
In order to get MySQL use multiple core for InnoDB, you must use the new settings that came with the InnoDB Plugin starting with MySQL 5.1.38.
Rather than reinventing the wheel, here are my earlier posts on this subject for InnoDB

Mar 16, 2012 : Using multiple cores for single MySQL queries on Debian
Sep 20, 2011 : Multi cores and MySQL Performance
Sep 12, 2011 : Possible to make MySQL use more than one core?
May 26, 2011 : About single threaded versus multithreaded databases performance

Give it a Try !!!