The Apple TV app doesn’t really care about directories. The app uses its own internal library database, to store local links to media files. That library database is also used by the Apple Devices app. Please add content in the recommended way only (drag-and-drop to Library view, or through the menu option of the Apple TV app). Remove any previous instances in the Apple TV app first before you add replacement/updated media for matching content.
By default, the app will copy added content in a designated directory on your computer, using its own naming conventions. You may choose to not do that (configurable in Settings﹥Files﹥) if you prefer your own media storage directories and/or original filenames elsewhere. Changes apply to new additions only.
For syncing to devices, you can check ☑ content in list mode to select what should be synced and what not. Exact duplicates (i.e. previously synced) present on both source and target devices should be skipped automatically when syncing. Duplicates on the source device should be managed first, so that only one of them gets synced.
Apple Devices app user guide for Windows - Apple Support
Apple TV app user guide for Windows - Apple Support
On Mac, it is also possible to sync just one specific media file from the Library at a time, for situations where that is more convenient. Not sure if the same is available through the Windows app.