You can indicate the "partial rollover" back to your IRA in the screens after the 1099-R entry screen.  To return to your 1099-R and indicate this, please follow these steps:

1. Click on Federal > Income & Expenses
2. Scroll down to the Retirement Plans and Social Security section and click on the Start/Revisit box next to IRA, 4701(k), Pension Plan Withdrawals (1099-R). 
   
3. If you have already entered this or other 1099-Rs, Your1099-R Entries, click on the Edit link next to the applicable IRA.
   
4. Click Continue on the 1099-R entry screen.
5. If you haven't yet entered this 1099-R, continue through the screens to enter the information.
6. After the 1099-R entry screen, you will see a screen What Did You Do With The Money From IRA?   Mark the button that you moved the money to another retirement account. 
7. In the section, Choose which of the following applies, mark the radio button next to: I did a combination of rolling over, converting, or cashing out the money.
8. In the next section, enter the Amount rolled over to another (or back to the same) retirement account -- the amount your IRA manager put back.
9. Continue through the screens to finish the 1099-R entry.
   

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