You must have misunderstood something. Taxes owed can Never be paid from a tax refund, federal or state.
In the File section on Step 2 of the program you were given several options on how to pay the federal taxes owed, paying from the state tax refund was Not one of those options.
You can pay the federal taxes owed using the IRS payment website for Direct Pay - https://www.irs.gov/payments
