In the Estimated Tax Worksheet, Part III, there is an area just above Part IV that says "Electronic Funds Withdrawal of Estimated Tax Smart Worksheet (Electronic Filing Only).

If you have the box checked next to Installment Number 2, it should reflect the June 15, 2021 estimated payment as being paid by electronic funds.

After checking the box, review the client letter to be sure it will come out automatically on June 15th.

If it still does not reflect the payment in the letter, review all of the boxes that are checked in Part I of the Estimated Tax Worksheet.  Sometimes answers to some of those questions will prevent the estimated payment from being made.