Sorry for late answer (I am back in EU since today).

Yeah, folders are shown on the emulated amiga as floppys - dont know if I can install
WB into this - I mean - normally you would have to format and partition a harddrive (emulated or real)
to install WB to, right?

No - it's much easier as you think!
Just make dir and copy the content of your Workbench inside! UAE reads those dirs. Host-harddrive can formated in any filesystem, which MOS can read.
Then point Sys to this directory in UAE-Prefs

filesystem=rw,Sys:Work:UAE/Sys_uae

This points to my 3.1-WB, installed in directory UAE/Sys_uae on my drive named Work:
In UAE it appears as "Harddrive" named SYS: and boots from there.