there are two penalies to consider
1) penalty for paying what you owe after the April 15 deadline
2) penalty for submitting the tax return after April 15 deadline.
The extension only covers #2. You get an extra 6 months for submitting the paperwork without incuring a "late filing" penalty.
However, that extension does not cover #1. The payment is due on April 15. If you don't know how much you owe (because you haven't completed the tax return!), then you are to estimate as best as possible. Any late payment penalty is only calculated on the Amount Due, which is after applying the estimated payments.
many get confused by the extenion.
This answer has been verified for accuracy by an Intuit expert employee
