Fixing Metadata for an Anime

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For #2: You need to alter your Sonarr config if it's not renaming files to your needs. I'd recommend looking to those communities or to their thorough documentation for information on renaming files on import. This is a basic function of Sonarr and not the focus of this community, so the line we (read: I) walk is to point you towards the resources that exist elsewhere.

On the Jellyfin side of things, you can either have Sonarr store its metadata in a Jellyfin-compatible NFO file (or not) or have Jellyfin store metadata in NFO files (or not). You can also edit the metadata individually (per episode) or in bulk by refreshing and choosing how you'd like to replace the metadata (missing only or replace all). If your naming doesn't match the required conventions of Jellyfin, you'll likely get some outliers you'll have to fix by hand.

To specify a metadata provider, you have to edit the Library, not an individual series. You edit the Library, enable or disable metadata provider(s), and rank them based on preference. For instance, anime libraries tend to benefit from using anime-only metadata providers such as AniDB and image fetchers such as fanart. All of that needs to be configured at the library level, not the series level. Then you can return to the series, click the kebab menu, refresh metadata, replace all metadata, and see what happens.

Jellyfin won't delete your files (unless you placed them inside your transcode directory as we all learned from a special, angry user a few weeks ago). It will delete the existing metadata, but that can be restored by refreshing in Jellyfin or in Sonarr and utilizing the source of your choice.