On your tax return you report the amount in box 5 only. Box 5 is the result of box 3 minus box 4.
To enter Social Security benefits reported on form SSA-1099
Click on Federal Taxes (Personal using Home and Business)
Click on Wages and Income (Personal Income using Home and Business)
Click on I'll choose what I work on (if shown)
Scroll down to Retirement Plans and Social Security
On Social Security (SSA-1099, RRB-1099), click the start or update button
Or enter ssa-1099 in the Search box located in the upper right of the program screen. Click on Jump to ssa-1099