Trying to get a pdf linked to its citation and it's going to "misc"?

No proble,. Then just make sure the checkbox “Store and search files relative to library file location” is checked.

I guess my question is, what should the “more or less standard” setting be for daily driving of Jabref and “automatic” attachment of the full text articles???

JabRef is able to do this via “Search for full text online” and can do this on import as well, if you enter a new entry by DOI for example. The file will then be stored in the right directory.
But sometimes the publisher change their websites and JabRef is no longer able to find the pdfs.

Manual adding:
JabRef has cleanup actions (Quality-> Cleanup) to automatically move and rename the file to the right directory. Or just a right click in the file field.

You might want to check Quality-> “Automatically set file links” for linking the files to the entry.

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