When you are adding a second Form 1099-R by clicking the + Add Another 1099-R link, there will be an option to choose whose 1099-R you are entering on the same screen where you indicate what type of Form 1099-R you are entering.
If you missed that entry, you can go back and edit the entry to change the ownership of the form. Use the following steps to get to the list of Form 1099-Rs that you have entered:
On the top row of the TurboTax online screen, click on Search (or for CD/downloaded TurboTax locate the search box in the upper right corner)
This opens a box where you can type in “1099-R” (be sure to enter exactly as shown here) and click the magnifying glass (or for CD/downloaded TurboTax, click Find)
The search results will give you an option to “Jump to 1099-R”
Click on the blue “Jump to 1099-R” link
Click Edit beside the one you need to change
Change the ownership of the 1099-R form on the first screen