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You can't change your payment method on your tax return if you have already e-filed AND it has been accepted. If it gets rejected, just log back in and make the necessary changes.
If you pay the IRS directly on their website before your original automatic withdrawal date, they will not deduct your payment a second time.
Per the IRS:
Pay Taxes by Electronic Funds Withdrawal: https://www.irs.gov/payments/pay-taxes-by-electronic-funds-withdrawal
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