Retirement tax questions

The company that initiated the rollover would be the only one that would issue a Form 1099-R, as was done in this case apparently.  You said you had a Form 1099-R reporting the distribution from your ROTH account and another one reporting the distribution from your traditional account. In TurboTax, the ROTH distribution would be entered as a rollover from a ROTH retirement account to a ROTH retirement account and the other one a conversion of a traditional retirement account into a ROTH account. Thus, the funds from the traditional account will be taxed and the funds from the ROTH account will not be taxed.

So, enter both 1099-R forms in TurboTax, in the Retirement Plans and Social Security section. Then choose IRA, 401(k), Pension Plan Withdrawals (1099-R) and enter your forms. On the screen that says What Did You Do With The Money From (Name of Payer) indicate that you moved the money to another account and that you did a combination of rolling over, converting, or cashing out the money. Then, enter the amount you converted to the ROTH IRA account, which would be the amount listed on your Form 1099-R reporting the distribution from the traditional retirement account.