(Quick & Dirty. Think Pascal, with its outlawed Writeln-Textwindow)
The question was: "I need to write an external file system for floppies formatted like MS-DOS floppies, but with a different directory structure on them."
The answer was: "Don't even think of writing an external file system (now)!".
Instead, convince yourself that reading and writing physical sectors on MS-DOS floppies is easy, and that you can implement the required functionality within your application (as Apple File Exchange does).