You only report the amount of Social Security benefits received using box 5 of the SSA-1099. Box 5 is the amount 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