If I overcontributed to my IRA accounts, should I leave the money and be taxed at 6%? Or withdraw, but pay the 10% penalty for being under the age

A 6% penalty applies each year until the excess is resolved.

Income tax and 10% penalty only apply to the earnings that are required to be distributed with a return of contribution before the due date of your tax return.  If the earnings attributable to the excess contribution are large, say 30% or more, it may be beneficial to pay the 6% for 2016 and make a corrective distribution in 2017 after October 16 when the earnings would not have to be distributed.