According https://www.naps2.com/doc/org-use (please, read the entire page):

Configuration
You can configure NAPS2 for your users by deploying application-level configuration files to the NAPS2 installation directory (%PROGRAMFILES(X86)%\NAPS2).

There are two configurable application-level files:

profiles.xml
appsettings.xml

profiles.xml
This file stores a list of scanning profiles. It acts as a set of default profiles that new users start with. If no application-level profiles.xml file exists, new users will start with no profiles. Note that once a user makes a change to any profile, changes to the application-level profiles.xml will no longer have any effect for that user. If you'd like to change this behavior, use the LockSystemProfiles element in appsettings.xml.

The user-level profiles are stored in %APPDATA%/NAPS2/profiles.xml. You can use your copy of this file as a base for the application-level profiles.xml (they use the exact same format).