You only input IRA contributions under Deductions and Credits. The retirement plan contributions on your W2 are not IRA contributions. So, entering under IRA contributions would not be double -counting... it would simply be incorrect.
If you contributed to an IRA, you would not have done so through your employer (except in rare cases). Your W2 may have a 401(k), 403(b), 414(h) or similar contribution. These are accounted for simply by typing in your W2.
