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After you file
Maybe you did not pay the whole amount that you actually owe when you sent in an estimated payment. We cannot see your return.
When you requested your extension you were supposed to pay your estimated tax due. Did you enter the payment you made into your tax return? Go to Federal>Deductions and Credits>Estimates and Other Taxes Paid>Other Income Taxes
If you have federal tax due you can pay by mailing your payment with the 1040V voucher, (which has the address printed on it, having the payment taken out of a designated bank account, or you can pay directly on the IRS website.
https://www.irs.gov/payments/direct-pay
https://ttlc.intuit.com/community/tax-payments/help/how-can-i-pay-my-federal-taxes/00/26212
You must pay your state tax due using the state’s preferred method of receiving payment. For most states that will be by making a payment to the state’s own tax website, or by mailing a check or money order.
https://ttlc.intuit.com/questions/1901670-how-do-i-contact-my-state-department-of-revenue
To apply for a payment plan with the IRS
Apply Online for a Payment Plan