ACH Universal can write back a unique reference number to QuickBooks, using a different numbering sequence--even alphanumeric (such as ACH100, ACH101, etc.).
 
This enables you to run ACH transactions first.  Then, when you go to print vendor checks, those processed by ACH Universal will have a sequence number in the register and will not appear in the list to print.
 

Note: This feature is designed for Vendor payments.  Employee payroll checks cannot access this feature due to security set by QuickBooks.
 

One-time Setup

From within the QuickBooks Integration Window, click on Settings > ACH Settings > Other Settings and check the box as shown below.
Want to set additional options?  Click on the blue 'Write back Options' link, and this will open the settings screen (2nd screen shot).

Write Back Options

Tip:  If you want to be able to identify ACH vendors when looking at the Vendor Center, you might want to add an asterisk or other symbol at the end of their name.  (ACH Universal uses the 'Print Check As' name by default by when pulling data from QuickBooks, so the asterisk will not show.)