So, I guess what I want to do is split on the commas, as long as they are not contained inside a set of parenthesis. I am lost on how to accomplish this with a regex.

This is easily accomplished with a regex (and the m// operator), but not so easy with split. What you want to do is parse SQL, and the best way to do that is not to do it :) meaning use the CPAN or SQL::Statement.

update: stricken extraneous bs. split or m// its all the same, you still have to parse the SQL.