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The eFile Center, in most cases, does not start submitting the filings to the appropriate agencies until a week before the due date. So, even if you submitted it to the eFile Center at the beginning of the month, it may not be processed by the state until closer to the due date.
Once the eFile Center has submitted the payment to the agency, they will then process the payment and take the money out of the account directly. If it is past the due date of the payment and it still has not cleared the bank, confirm the filing status at https://efile.aatrix.com/, on the Filings tab. If the filing status is CLOSED, contact the agency to see if there is a delay in processing the payment.