Used TT deluxe and provided direct debit info for the taxes that I owed to IRS. Later, for a reason, I used IRS direct pay to pay early. Will I end up paying double now?

See this IRS website for cancelling the direct debit payment - https://www.irs.gov/uac/pay-taxes-by-electronic-funds-withdrawal

• Once your return is accepted, information pertaining to your payment, such as account information, payment date, or amount, cannot be changed. If changes are needed, the only option is to cancel the payment and choose another payment method.
• Call IRS e-file Payment Services 24/7 at 1-888-353-4537 to inquire about or cancel your payment, but please wait 7 to 10 days after your return was accepted before calling.
• Cancellation requests must be received no later than 11:59 p.m. ET two business days prior to the scheduled payment date.

So, I should assume that after I paid in full, using direct pay at IRS website, I am good even though I e-filed? And just cancel my direct payment associated with e-file, scheduled for a later date in April?

Yes, that would be a valid assumption.  You will have your bank statement showing the payment to the IRS when you used Direct Pay.

Thank you! I'll go ahead and cancel it then.