Just make the second 20gb partition FAT32 or let windows format it for you when you use the windows boot disk.

Is the 20gb Windows partition you are refering to going to be used for the OS? Why not load Fedora on the 4gb drive and windows on the 40? Changing between OS's would be as easy as changing the boot order in the bios (i.e. HDD0, or HDD1).