No, IRS will only accept one extension. But forgetting to adjust the taxes owed won't invalidate your extension; you'll still have it.
If you think you'll owe and you want to make a payment, you can do that separately from the extension. Just write the check to "US Treasury" and include your SSN, "tax yr 2016," and "Form 4868," so IRS knows what the payment is for.
Here's the link for IRS mailing addresses, which depend on what state you live in: https://www.irs.gov/uac/where-to-file-paper-tax-returns-with-or-without-a-payment . Click on the link for your state, and you'll find the mailing address for the Form 4868 (the extension form). Choose the "payment" address shown for that form, even though you won't be mailing the actual 4868 itself, since you filed it electronically.
If you get it postmarked today, you'll have made the payment deadline.
