Since the IRS is short on personnel the returns with balance dues on them have been put to the back of the line and can take months to process. Until they are processed you may not be able to make a payment online on the IRS website ... if that is the issue then you can either wait for the bill or mail in a payment with a 1040-V.
https://www.irs.gov/pub/irs-pdf/f1040v.pdf
