[For QuickBooks Desktop only]

ACH Universal can write back a unique reference number into the QuickBooks register, using a different numbering sequence--even alphanumeric (such as ACH100, ACH101, etc.).
 
First, you will pay all bills in QuickBooks and mark them 'To Print'.

Then, you will open Treasury Software and click on the QuickBooks Integration icon to create the ACH file.  Only vendors with banking information on the profile will come over into the 'window', and you will create the ACH file.  The write back feature will start, and numbers will be assigned automatically.

After creating the ACH file, you will print the remaining checks that are still in the print queue in QuickBooks.  Those processed by ACH Universal will have a sequence number in the register and will not appear in the list of checks to print.
 

One-time Setup

If using the version 2023 software:

From within the QuickBooks Integration Window, check the third checkbox to 'Write back reference numbers'.  (You will need to do this in each account/database that was set up.)

If you click the blue link for 'Write back options', you can change the reference number template.  Canadian clients could use the reference 'EFT100', etc.

Notes:
1. This feature is designed for Vendor payments.  
Employee payroll checks cannot access this feature due to security set by QuickBooks.
2. This feature supports 'Automatically create a transmission file' (default) only.  It does not support delayed file creation. See QuickBooks Integration > Settings > Common Settings > 'When clicking on Send transactions to ACH Universal'.

If using a version of the software prior to 2023:

From within the QuickBooks Integration Window, click on Settings > ACH Settings > Other Settings and check the box as shown below.
You can click on the blue 'Write back Options' link, and this will open the settings screen (second screen shot below).

Here you can choose the sequential number that will appear in the bank register.  By default, it is set to create 'ACH100', but you can change it to 'EFT100', or whatever numbering system you wish to use.  Note:  If using more than 6 characters, the last numbers will not be displayed in the bank register.

Employee payroll:  You will assign ACH payment numbers when running payroll

Intuit does not allow third-party apps to write back (as above) to payroll items in QuickBooks, but it is possible to 'Assign check numbers' in the payroll check options, and enter an 'ACH number' when running the payroll.
This number will automatically sequence when processing.

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