Sometimes it does take a bit longer for the IRS to update their website. Since you have a balance due based upon your tax return as filed, make the payment that is due by April 15th to avoid any late payment penalties.
Please see tax payment options from the IRS for all of the options you can use to pay your tax due as reflected on your tax return. Be sure to include all information as prompted to ensure your payment is applied to your account based upon the tax return filed.