Hi Stu and thanks for your interesting post!
Honestly, I would never think that in 2022 someone new would jump into AmigaOS. Wow, respect!
Despite the following chapter from FAQ does not necessarily apply to you, I'll paste it here anyway:
If you're completely new to Amiga world, or you owned an Amiga back in the times and now you would only like to play some games again and nothing else, well, while that is certainly possible with AmiKit, there are probably more simple solutions for you (check Amiga Forever, for instance).
AmiKit aims to provide a full AmigaOS experience and beyond. That involves enhanced operating system capabilities and features. And while we made everything as easy as possible (everything is pre-installed and pre-designed), some basic Amiga knowledge is required to fully enjoy (and appreciate) the AmiKit package.
Anyway, before you start experimenting with AmigaOS/AmiKit, I strongly recommend to backup AmiKit folder in Manjaro Linux (simple Ctrl+C/Ctrl+V will do). If anything goes wrong later, simple restore the backuped folder and you're back on track without re-installing anything.
Here's a basic info about Amiga Workbench: https://en.wikipedia.org/wiki/Workbench_(AmigaOS)
Note that AmiKit is based on 3.x version. And it uses Directory Opus Magellan II on top of it to improve user experience.
A quick googling revealed the following videos about Amiga Workbench for beginners:
Part 2: https://youtu.be/ylnMKwSfC4Q
However, on those videos you can clearly see how much AmiKit differs from default 4-color AmigaOS Workbench. Perhaps you could check some of my tutorial videos instead, even though they don't cover many areas: https://www.youtube.com/playlist?list=PLxEnP5UUSCcREBN5C0aCC-zZ5H_gK4FTV
Regarding your specific question, no, there's no «user» folder anywhere. Feel free to create one anywhere and store your data there
Hope it helps?