DigitalVolcano Software Support

I normally copy files (mostly photos) from an SD to a disk and then organize these files on different folders. I sometimes delete
the files from the SD once copied, but not always. Also, sometimes I forget to copy from the SD to the disk. I want to use Duplicate cleaner
to compare files in the SD to files in the drive across folders so that I can identify any file that has not been copied, or,
identify all files that have been copied and then delete those. Note I do not want to identify duplicate files
within the disk, just want to compare those in the SD.
How should I set the options in Duplicate Cleaner?

Try using the Wizard for comparing disks ("Compare drives or folders to find missing or changed files"). This will also give you an idea of the settings.

Tried, thanks. Some doubts:
1.Should the SD go as "A" and the disk to "B", or the reverse? Or it just does not matter? Note I am not interested on duplicates within the disk (in this particular case, which will be very common).
2. What do I have to do to display duplicated files in the SD only, and delete those files making sure the disk is not touched?

1
SD would be 'B' (i.e. the drive that you are trying to compare to the other drives/folders to find missing files). The missing files on 'A' will show in the 'Remaing/unique' tab.

Always back up first!

2, Not sure what you mean exactly, but you can protect a drive or folder from deletion by setting it to 'Protected' in the 'Folders to search' pane.