Ulysses is not a filing app for web stuff. I imported recipe files i collected — Evernote > Ulysses. The results for non text files were a mishmash of sorta worked. (I keep reading about DevonThink)
My general Ulysses organization .
Darn the wrong link will correct later.
I’ve used OneNote. Fine app… Basically I’m not filing and storing as much stuff. The joys of the simpler life.