Want to pay some vendors by paper checks - and some by ACH?
Yes, it's easy to do with ACH Universal.
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 not print paper checks.

Note: This feature is designed for Vendor payments. Employee payroll checks cannot access this feature due to security set by QuickBooks.
One-time Setup
Turn ON - From within the QuickBooks Integration Window, click on Settings > ACH Settings > Other Settings and check the box below.
Want to set additional options? Click on the 'Write back Options' - and this will open the settings screen (2nd screen shot).

Write Back Options
