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Usually when they are deducting from your paycheck it is for a 401k or 403b---not an IRA. You only enter it by entering the information from the boxes on your W-2. Do not go anywhere else in the software to enter it again.
No, if it is deducted from your paycheck, the pension contribution will show on your W-2 form as a deduction from your wages reported in box 1. It will likely be referenced in box 14 on your W-2 form as well. You will typically notice that your wages reported in box 1 on your W-2 form is less than the social security wages reported in box 3 and the Medicare wages reported in box 5. An IRA contribution would be something you did on your own, outside of what you did through your employer.
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