When you install Linux, the installer will prompt you about installing the Bootloader (GRUB used for Fedora).
Have you been able to boot Linux at all?---eg by switching the boot order in the bios? The way you describe it, GRUB may be on the mbr of the Linux drive--in which case you would have to set the BIOS to boot that drive first.
Otherwise, you will need to boot from the Fedora CD in rescue mode and get into Linux that way.
Once you are in Linux, you can install the bootloader on a floppy--or on the mbr of the Windows drive. Here are the commands---assuming that Windows is on the first drive, and Linux on the second:
grub #puts you in the grub shell
root (hd1,0) #assumes that Linux is on the 2nd drive, 1st partition (grub counts from 0)
setup (hd0) # to put grub on the mbr of the 1st drive
setup (fd0) # to put it on a floppy
Eventually, you will want to get a copy of the GRUB manual http://www.gnu.org/software/grub/manual/grub.html
Consider installing Windows and Linux on the same drive--the samller one--and using the large drive for shared data. Format it FAT32 and it will be easily accessible from both Linux and Windows.
Also consider getting Fedora 5 instead of 4.