Before making an additional payment, I would try and determine why a payment wasn't taken. If it is only a few days, your return might not be processed yet. Or, maybe you used the wrong bank account number or had a typo.
If the payment is just slow, you risk having the IRS take the payment anyway, on top of your manual payment. They will eventually return the difference, but it may take a few months.
If you used the wrong number for your bank, you can expect that the IRS will add a "bounced check" fee to any interest and late fees you might owe.
