If you want to have Linux on a separate drivew, then all you need to do is to AVOID automatic filesystem setup, go into the partitioning dialog, make sure to UNCHECK the drive with Windows (so that it's not used for Linux) and assigning the other drive to Linux. The Fedora installation tools provides enough hints and infos during installation to work out the remaining details.
Make sure to install the Linux booter on the same drive where Linux is. Overwriting the MBR record on your c drive could make Windows unbootable (can be repaired, but it's tricky). You HAVE TO get you hands on some tutorials for dual-booting system setup for tips on how to boot into Linux without modifying your BIOS each time.