There is no need to use file-sync rule.  Just get the list of script command required to set all the required registry key/values and use send script to apply to targeted device(s).

Based on the online manual at https://soti.net/mc/help/v14.5/en/scriptcmds/reference/windowsmobile.html ,  you can use the following command to set registry value

    regset registryKey [valueName] [data]

If you insist on using file-sync rule, just add one, and paste the script content in the "Before file synchronization execute script" field after clicking on the "script" button in the advanced tab.  I usually choose "Download file(s) from Server to Devices" for the file-sync direction, and add a dummy empty server directory to ensure that no bandwidth is wasted on actually downloading any file.