xplorer² duplicate checking engine doesn't care about locations. All it needs is a scrap window with a collection of files, then it checks the files present for duplicates. The simple Check duplicates menu first flattens the local folder hierarchy, extracting all files in all subfolders, then uses the command parameters to discover duplicate files. A naive approach would be to flatten all the files and folders in your system starting from My Computer folder, and check for duplicates among all your files — but that would take ages. If you know where the files reside (approximately), it will be much better to extract only the folders involved, narrowing the number of files checked.
Let's say you have music files under C:\MUSIC and D:\TEMP\AUDIO. To check duplicates in these 2 folders, browse flat the first one (use the command in File menu), extracting all its contents in a scrap container window. Then select the second folder, drag it with the right mouse button and drop it in the same scrap container, and pick Browse flat command from the context menu. Now you have all the files to be checked, from both C: and D: locations, in a single collection; all that's left is to click on the Duplicates toolbar button in the scrap window to start the checking. If you have more folders to check just add them flat to the collection with right-dragging.
TIP: If you have many folders to flatten it may be easier to do it in two steps: first put all the folders (normal, not flat) in a scrap container, then use View > Dual pane menu to turn on the second pane in the scrap. Select all the folders in the left pane and press <Alt+Return> key combination. Presto, all the folders will be flattened in the right hand side pane!
Remember working in a scrap container, pressing <DEL> key doesn't delete files, only removes them from view. To remove the duplicates from disk use File > Delete menu command.