When you enter the 1099-R, you answer all the follow up questions and indicate how much of the withdrawal was rolled over to an IRA within the 60 day limit for making a rollover. On form 1040, the amounts on lines 4a or 4c should show the total distribution amount and the amounts on line 4b or 4d would have the taxable amount which is the total minus the amount rolled over. The word rollover should also appear somewhere near these lines.
