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I put them in a separate jellyfin generic media library and name them with chanelname - video title.
Then i sort by date added to simulate the YouTube subscription view.
I remove what i watched and dont fancy keeping. Ive considered re organizing videos i keep into their own series.
Three options you could explore: Tube Archivist (with plugin), Pinchflat and Toothpick.
(No personal experience in using Toothpick)
Create a separate library for YouTube contents, then TA or PF will create different 'shows' inside it. The TA plugin or PF built-in option to generate NFO files will prepare all metadata necessary for Jellyfin import. To separate the channels, you simply set them up separately in TA or PF then they will show as different 'shows'. All these GUI applications are built on top of yt-dlp by the way.
You can check out something I made to help me grab and organize things like this, can help with artwork too if you find a good thumbnail:
I have a folder called "Let's Plays" with sub-folders like so:
In each of those folders I have folders for each "season" (for long-going series the seasons are by year (Season 2024) but are otherwise "season 1")
Then the videos/thumbnails themselves are like this:
untouchedwagons@storage:/mnt/tank/Media/Videos/Let's Plays/R/Rimworld with Mr Samuel Streamer - Mushroom Madness$ ls *
'Season 1':
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E01 - The Mushroom Apocalypse.jpg'
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E01 - The Mushroom Apocalypse.mp4'
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E02 - Taking Back the City.jpg'
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E02 - Taking Back the City.mp4'
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E03 - How Far Would You Go_.jpg'
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E03 - How Far Would You Go_.mp4'
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E04 - Scientific Breakthrough.jpg'
'Rimworld with Mr Samuel Streamer - Mushroom Madness - S01E04 - Scientific Breakthrough.mp4'
In Jellyfin I have a library for these Let's Plays that are separate from my regular TV Shows.
I use JDownloader 2 to download youtube videos. I normally only download two to three videos a day so doing it all manually isn't that big of an ask, though editing metadata on mkv's is a bit of a pain.