When a QuickBooks user has both checks and ACH payments to process, we recommend that the ACH vendor or employee names be marked with an asterisk (or other symbol) so they are easily identified. Or, you can setup a separate Accounts Payable specifically for ACH transactions.
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.
Run ‘Pay Bills’ as usual (with no specific knowledge of who is receiving an ACH or check).
Integrate with QuickBooks and create an ACH file. Only the vendors with banking information filled in on their QB profiles will come over to ACH Universal when integrating.
If you have selected the 'Write Back' feature, the bank register will be populated automatically with sequential ACH numbers.
Then, when you are ready to print 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)