They will use the bank account you have included in your installment agreement. You do not have to write a check. The IRS usually debit the date you specify when you made the payment. If you did not select a date, the IRS will withdraw the payment April 18th 2017. If it is not taken by this time you may want to call the IRS customer service line at 1-800-829-1040 to inquire regarding the status.