What if youve made your contribution to your ira thru your employee 401k payroll?

No. IRA and a 401(k) are different. If you have an amount on your W2 with Code "D" in Box 12 - that's a 401(k), not an IRA. You don't enter that amount anywhere else on your return. 

IRA contribution are not through an employer. If you made an IRA contribution follow the instructions in the  below to enter your contribution:

Where do I enter my traditional or Roth IRA contributions?