I usually scan my media with Media Elch before I move it into Kodi/Jellyfin then I know the files and folders have the right names and all Metadata is correct.

TV shows are grabbed, named and tidied with pyMedusa.

I use Kodi on a RaspberryPi with the Jellyfin add-on so if I watch something remotely then the watched status is synced everywhere.

If you’re using Windows then Foobar 2000 is great. I use it for manually managing and tidying my collection in addition to converting pretty much any format to any other format.

That being said, you can install it as a snap in Linux as well if that’s your poison.