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The Preference Panel can be opened by choosing Preferences… from the dittoGUI menu, Command-comma.
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Preferences Window

When Append to Source is checked, you can repeatedly drop new files onto the Source drop zone. This enables dragging from different folders and drives. If this is unchecked the new drop will replace the files.

It also displays the Clear button, this is because if you make a mistake and drop a wrong file there is no way to remove the Source files and folders.

Clear Source after ditto clears the Source Files list after ditto has finished its task. The Source file list is not saved for later use.

Remember Destination will save the destination folder and later restore it when the App is opened. when you uncheck this option it does not forget the save folder and when it is later enabled it will restore it. This can come in handy for doing some ad hoc work then recovering the saved Destination.