Some of the OS resides in the built-in rom chip, but many essentials are on the Workbench floppy. Example: the commands in C:, the files in LIBS:, DEVS:, L:, S:, etc. In the early days before hard drives were common on Amigas, people were very creative about ways to work with only 1 or 2 floppy drives. The extreme flexibility, small footprint, and logical structure of the OS contributed greatly to it's lasting popularity. You probably knew this already!
Most people make a copy of their original Workbench disk and delete from the copy those utilities, commands and programs they won't need everyday. This will free up some disk space for your preferred programs.