If you are filing an extension, usually it asks what your best guess is on what you owe and when you expect to pay. I usually send an extension through the mail so that I can include a small payment by check. I push my pay by date out by a few months. If you can pay your taxes owed in full now, you should not have to file an extension. An extension does not cancel accumulating interest costs or penalties as far as I know. It is a convenience that serves you best if you need additional time to get your documentation together and you do not expect to owe taxes.
