I would approach it this way:

1. Learn to configure and install Jellyfin the way you like it. You sound like you have a good start on that. JF handles metadata for you, and you can also manually match items if/when it matches up. The only extra plugins I install are some of the ones for extra metadata providers and TMDB box sets.
2. Setup Jackett with the qB search so you can run manual searches for stuff against your indexers.
3. If you want to use docker, learn docker. There’s a million tutorials around. You can use Docker Desktop on Windows if you want a GUI to help you out. Since docker on Windows runs on WSL2, it’s a good opportunity to mess around with Linux if you aren’t familiar.

From there you can work your way up to full automation and such if you like. I don’t think it’s necessary for most people.

As for data layout, just make some folders like movies, tv, music, etc, and lay out stuff in there logically. If you have a fancy storage setup, you might do separate shares for them, whatever works for you. Some people like to link from their “download” folder into their actual media folder to keep things clean. You can do hard and soft links on Windows with NTFS, but it’s kind of a pain.

https://trash-guides.info/

This doesn’t cover Jellyfin but the rest of the stack the gets files into it. And frankly I disagree with a number of the ways that they do things but if you want a guide that gives you a setup that works with a community that is helpful (they have a well populated discord) this is a good starting point

Jellyfin is basically install it, create a library within the app, point said library at a folder on a drive somewhere with media on it.

You generally want to follow reasonable naming conventions, eg showname.s01e01.mkv but these have gotten fairly flexible over the years. You don’t need to worry about the extra stuff like webdl.1080p.flux.proper etc, that is typically ignored, though there are always edge cases. The bigger headache is making sure your files match thetvdb or themoviedb as this is primarily what Jellyfin will use for scraping. If you use sonarr/radarr you can ensure the files are properly ordered and even rename them to scrape perfectly but this can be a headache for seeding if you torrent as renaming the files will break shit. This gets you into needing to hardlink if you want to keep things automated unless you want to manually go in and rename the files in your torrent client which is a chore, the trash guides describe how to set this up

Anime can be a chore, especially older releases, because lots of good shows were released by random people and not groups. As a result they decided to just release things with sequential numbered episodes (eg instead of s01e01,02, etc it’s just a folder with 1.mkv, 2.mkv, etc). Or they released them with episode numbering that differs from what tvdb has because they insist that some other source like anidb is gospel. Certain western shows can be a nightmare because of stuff like this too (American dad is the worst)

From there it depends on how you want to customize your Jellyfin install. I use a kodi as a front end so the only plugin I bother with is Jellyfin for kodi. But before that when I used native clients I used jelly scrub, introskipper, etc. but a lot of those plugins are redundant now because they’ve been built into native Jellyfin.

You also may need to set up transcoding. This depends on your setup. My setup direct plays everything (ugoos streaming box with Coreelec/kodi). This is really only necessary if you have a setup that benefits from the direct formats, eg a surround sound setup, oled screen that can play dolby vision or a led that can do hdr10+, etc. or if your server is really garbage and can’t handle transcoding. But really it has to truly be awful; intel quicksync going back years can handle most modern files pretty effortlessly (unless you start messing with stuff like av1 or vp9), nvidia transcoding also works fine even with relatively old cards (though using much more power by nature of needing a gpu installed). If you have an amd cpu video core next works too although quicksync is objectively superior, though not necessarily enough to justify buying a whole new setup and creating a bunch of waste when your amd rig will work well enough.

As you can see transcoding is in and of itself a diverse topic and how you set that up depends on your setup and needs: what’s your hardware, do you need tonemapping, how many concurrent streams do you anticipate having, etc.

It sounds like a lot but if you play with it for like a weekend you’ll be fine and then you’ll be free of streaming bullshit and the associated data collection

Docker isn’t needed for Jellyfin. It can be just installed like a regular program. I don’t know about any Arr stacks but Jellyfin by default will identify and fetch metadata for any media included in its library. The library structure that I use is one folder for music, one for TV shows, and one for movies. That’s it. I just copy over manually downloaded or ripped files.

I use Linux for hosting Jellyfin but the setup was minimal, it was just some Linux specific file permission stuff. Before you get too far into it just download Jellyfin and give it a try! You might be surprised how little setup is needed.

Most of us started with the TRaSH Guides.

Also it’s not Linux or Windows; it’s Docker (which works on both Linux and Windows).

Also check out YouTube. There are a lot of great tutorials on there.