Your mortgage balance should be the balance on the new (refinanced loan). There should not be a balance on the original mortgage as it was paid off by the refinanced loan.
If you have multiple 1098 mortgage forms, you’ll enter them one at a time. After going through the steps with the first one, you can add a lender when you get to the Mortgage deduction summary screen. (In the case of a refinance, it's best to enter the 1098 from your original loan before the 1098 from your refinance.)
Be sure to use the 1098 to enter your information so that the loan balances will be reflected accurately.