Users typically have a Backup folder of some kind. Files residing in this folder should not be suggested by a duplicate files finder. In DiskState, click on "New" from the "Duplicates" tab of the settings and select the folders containing files to be ignored by the duplicate finder.
A more advanced approximation of setting an ignore rule for duplicate files, is to use regular expression matches per file name. You can create, edit and remove these rules from the same tab as mentioned above. I.e. to ignore all the important duplicate Zip files on your computer, enter .*\.zip as your rule. Now, your zip collections will remain safe and no duplicate zip file will be suggested for removal.
These rules are stored in an INI file called Dupes.ini if you want to edit this manually. The format of this file is explained in the top of this file. It normally resides in the DiskState folder.