Yes. When correcting a previously accepted original return, you will report the refund that you received on your 1040X line 18 "Overpayment, if any, as shown on original return or as previously adjusted by the IRS." The 1040X will compute the additional tax that you owe due to the 1099. TurboTax will automatically report the original refund when you are amending a return previously filed in TurboTax, you do not need to manually enter the refund.
Here is a helpful article on amending returns: Amending Your Income Tax Return