In my 403b, I did an in-plan Roth conversion early in the year, and I did a pre-tax rollover into a Roth later in the year (plan does not allow more than 1 in-plan conversion each calendar year). The 1099R that I received showed both amounts together and all of it as taxable, which is what I expected. When entering into TurboTax, the only options I have are that the entire amount was converted (in-plan) or that the entire amount was rolled into a Roth IRA. It only affects how things are filled in section "B" on the 1099 R entry form (when I look at forms view). The end result is that the taxes are the same. However, I don't like that TT will not let me truthfully answer the interview question. TT is assuming that each 1099R corresponds to a single transaction, and maybe it doesn't matter, but it took me a little while to figure out that it doesn't make a difference. I'm using TT to reduce confusion, not increase it.
For entry into TurboTax, you'll need to split the Form 1099-R into two, one for the portion rolled over to the designated Roth account in the 403(b) and another for the portion rolled over to the Roth IRA. The only difference in the way TurboTax treats these separately reported rollovers is the recording on the IRA Information Worksheet of the Roth IRA conversion basis resulting from the rollover to the Roth IRA.
(Regarding TurboTax being a work-in-progress, splitting of the Form 1099-R under these circumstances has been necessary since 2008 when rolling over a distribution from a traditional account in a qualified retirement plan directly to a Roth IRA became permissible, so this aspect has been a "work-in-progress" for more than 10 years.)
Turbo Tax as comprehensive as it is doesn't cover all contingencies. As these issues arise, Turbo Tax does do a very good job of addressing these but keep in mind, it is still a work in progress. As old issues get resolved, new issues arise everyday.
For entry into TurboTax, you'll need to split the Form 1099-R into two, one for the portion rolled over to the designated Roth account in the 403(b) and another for the portion rolled over to the Roth IRA. The only difference in the way TurboTax treats these separately reported rollovers is the recording on the IRA Information Worksheet of the Roth IRA conversion basis resulting from the rollover to the Roth IRA.
(Regarding TurboTax being a work-in-progress, splitting of the Form 1099-R under these circumstances has been necessary since 2008 when rolling over a distribution from a traditional account in a qualified retirement plan directly to a Roth IRA became permissible, so this aspect has been a "work-in-progress" for more than 10 years.)