Given that these were from the same account, it seems that these must be distributions from the traditional account in the 401(k) , not from a designated Roth account.
The combination of the details of the Form 1099-R and the transaction details seem to agree that the check for $66,000 was to be deposited into the Roth IRA as a Roth conversion (technically a taxable rollover) and the check for $33,000 was to be deposited into the traditional IRA as an ordinary rollover. From your original question It seems that this is where the checks were properly deposited.
To report these rollovers in TurboTax, you must split the Form 1099-R into two. The first one will have $66,000 in box 1, $30,000 in box 2a, $36,000 in box 5 and code G in box 7 which you will indicate to TurboTax was not rolled over to a Roth 401(k) but was rolled over to an Roth IRA. The second one will have $33,000 in box 1, $0 in box 2, $0 in box 5 and code G in box 7 which you will indicate to TurboTax was rolled over to neither a Roth 401(k) nor a Roth IRA. The sum of the corresponding boxes on the split forms must be the same as the dollar amounts in the corresponding boxes on the form provided by the payer. On Form 1040 TurboTax will include $99,000 on line 5a and $30,000 on line 5b with a "ROLLOVER" notation next to line 5b.
