After you enter the Form 1099-R for the withdrawal, proceed through the questions in the Step-by-Step interview. One of the screens will ask you if you "moved the money to another retirement account." When you select that you did that, it will ask you for the details of the rollover. Answer that you "moved the money to another retirement account" even though you only rolled over part of it. One of the follow-up questions will ask you how much you rolled over.
