The debit can take up to 24 hours to show up in your bank account from the time the IRS initiate it, and it may take them a couple of days to initiate since it's the busiest day of the year.
When you're ready to pay the balance, the easiest way to make a payment is to go to www.irs.gov/payments and make an electronic payment. Make sure you select "2016 form 1040" as the reason, and not a prior year or 2017 estimated payments.