When you enter the Form 1099-R, indicate as rolled over whatever amount of the box 1 amount on this Form 1099-R that you deposited into another qualified retirement account as a rollover contribution. Enter the Form 1099-R under Wages & Income -> Retirement Plans and Social Security -> IRA, 401(k), Pension Plan Withdrawals (1099-R), then indicate that you moved the money to another retirement account and enter the amount you rolled over. TurboTax will exclude the amount rolled over from the amount reported on Form 1040 line 4b and will included the word "ROLLOVER" next to the line.
