If box 6 is empty on your SSA1099 you leave that blank when you enter the SSA1099. The "extra" money you are having withheld from paychecks from a W-2 job has nothing to do with the amounts you are seeing on a SSA1099.
When you enter all of your income including the Social Security and the W-2 income, the software will do the calculations and reconcile whether you get a refund or owe tax due.