After you enter your 1099-R(s) and see the list of 1099-R(s), when you hit Continue, you will pass through a series of screens. If you took a distribution that was possibly subject to an early distribution penalty, eventually a screen will appear that is headed "Let's see if we can reduce your early withdrawal penalty".
Click on Continue. If you make an entry on the next screen, this amount will appear on line 2 of the 5329. This is the amount of the distribution that is not subject to the early distribution penalty because it meets one of the exceptions.