if the first drive is windows ( sda) and set as master
then the second drive is set to slave ( sdb) linux
the fedora installer will ( default settings) install GRUB on the MBR of sda overwrighting the windows bootloader . Then will auto setup grub to boot windows and fedora .
there are two ways to dual boot
1) use GRUB to boot both windows and fedora ( default setting)
also you will need a windows install disk ( not a windows repair disk)
if something goes wrong
every know and then Windows WILL
try to " fix" the working GRUB and replace it with the windows bootloader ( say by by to booting fedora with out the install disk) until you reinstall GRUB
2) use the windows bootloader to boot fedora and windows
HOWTO Dual Boot Fedora & Windows With NTLoader
can be a bit risky if you type the wrong command , this is not very likely .
i use this method to boot win xp and fedora 8