On your tax return you enter only the amount from box 5 of Form SSA-1099. That would be the net amount of benefits that you received, after subtracting the repayment. On the amended SSA-1099 box 5 should be less than box 5 on the original SSA-1099 by the amount that you repaid. When you change the amount in box 5 to the reduced amount, TurboTax will recalculate your tax to adjust for the amount that you repaid.
