If your income is over a certain level, the amount of IRA contributions you are able to deduct may be limited or phased out completely. However, you can still contribute to your IRA using non-deductible contributions. Although your contribution will not aid in reducing your taxable income, the earnings will be tax deferred until you withdraw the funds.
The current rates for each filing status may be found in the Form 8606 Instructions found on the IRS website.
Any nondeductible IRA contributions will be calculated by the program and pulled to Line 1 of Form 8606 when you report your traditional IRA contributions under the Federal Section > Deductions > Adjustments > IRA Deduction.