Conceptually, you'll need 4 files.

main.c - the portable part of your application, and #includes port.h
port.h - your abstracted interface to your floppy, with say move_head(int track);
port_win32.c - implements move_head(int track) and the rest of the API, for win32
port_linux.c - implements move_head(int track) and the rest of the API, for linux. If possible, try to do this using the POSIX API as much as possible. It'll save time when moving to other POSIX systems.

When you build a system, you choose (in your project / makefile) the appropriate port_xxx.c for the environment in which you're working.

Do you have specific questions for specific platforms still?