I am doing a 3 year catchup on my IRA though my work. I am contributing more the the allowed amount. How do i enter this on my taxes to avoid the 6% penalty

The employer's retirement plan is not an IRA.  The type of plan that allows a special 3-year catchup is a 457(b).  Enter amounts shown in box 12 of your W-2 only in box 12 of TurboTax's W-2 form, nowhere else in TurboTax.  Remove the erroneous IRA contribution that you entered,