It is not possible to change the default setting to not print check numbers. However, this can be turned off during each check run using the steps below:
  1. In Banks, Select Print Check and Record Bank Drafts (In Payroll: Print checks and EFT notices)
  2. Select the Format tab.
  3. Mark or unmark the "Print Payment number" checkbox.
  4. Select Create Now.
Note: This selection is only for this payment run.  There is not an option to edit this for every payment run. 
The default selection is set to Print the payment number.