How do you enter repayment of SSA Benefits?

The repayments should be included on your SSA-1099.  The repaid amount is in Box 4.

Gross benefits (box 3)

Less repayments (box 4). Equals

Net benefits, in box 5 of SSA-1099 
 

As long as the amount in box 5 is positive, any repayment in box 4 is included in net benefits and need not be reported separately.

If you have to repay an amount of Social Security Benefits that you included in your income in an earlier year, you may be able to deduct the amount repaid from your income for the year in which you repaid it. This is explained in IRS Publication 915  Page 5, Social Security and Equivalent Railroad Retirement Benefits: