If you add an extension to a tax return that shows a balance due, the balance due shifts to the extension form and the return will show no balance due because the assumption is that you have made the payment on the 4868 form.
Whether you owe or not, the important thing is that the extension gets filed on time and if you do owe, you pay pay on or before the due date of April 18 (may be later for state returns).
If you don't really owe any tax, but you file a 4868 that says you do, that doesn't cause any problems. Tax can only be assessed based on a tax return or information that the IRS gets from third parties, like banks and employers.
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