Yes, leave the main drive as FAT32 - it's easier for transferring files from USB. I used that to move a pretty complete TOSEC collection of ADFs to my main Work: partition. You do need to use the linux command line for that though; you can get to it with Ctrl+Alt+F1 or F2.
Once there you need to reboot to get back to the Amiga, so make sure you've closed any apps that are running.
You can log in with user "root" and pass "root" for maintenance.
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