When a QuickBooks user has both checks and ACH payments to send out:
Run ‘Pay Bills’ as usual (with no specific knowledge of who is receiving an ACH or check).
If you are using 2018 ACH Universal software, turn on the QuickBooks ‘Write Back’ feature (by clicking on the QuickBooks Integration icon > Settings tab > then ACH Settings. At the bottom of the page, check the box and be sure to click on the blue link for ‘Write back options’. This will allow you to set the ACH sequence numbers that appear in the QuickBooks bank register.
Integrate with QuickBooks and create an ACH file (after the QuickBooks ‘Write Back’ feature is turned on). In addition to logging the payment, it turns off the ‘To Print’ indicator.
When printing checks, the ACH payments will not appear in the list to print.
The resulting sequence in the bank register will reflect the ACH numbers and the check numbers.
NOTE: Payroll checks cannot be marked with ‘Write Back’ (QuickBooks locks these down).