When you enter the Form 1099-R into TurboTax, TurboTax will ask what you did with the money. Assuming that you deposited the money back within 60 days and have not violated the one-rollover-per-12-months rule, indicate that you moved the money to another retirement account (or returned it to the same account), indicate that you rolled over part of the money and enter the $2,000 that you rolled back into the account.
