On 1099-R on box 3 Capital Gain......what goes there?

If you had an entry in Box 3 of your paper or electronic Form 1099-R, then that number goes in the Box 3 entry of the 1099-R interview. 

If there was no entry (or a "0") in Box 3 of your paper or electronic Form 1099-R, then nothing goes in the Box 3 entry of the 1099-R interview.