IIRC Turbotax tries to choose the right option for you by asking if this is the first return you file jointly. If you answer "No", you can input only a single AGI.
I believe I read in some discussion here that the answer you give to that question is not sent to the IRS, but I wasn't able to find it now.
Anyway, it was the second year of filing jointly, but the first we filed electronically. I just tried answering "Yes" to the first-time-jointly-return question and Turbotax gave me the option to provide two AGIs.
In our case everything was processed correctly, but I should emphasize that I don't really know if that is the "right" way to go.
