Best when using separate HD's to boot via the BIOS, to keep HD's independent and avoid GRUB corruption of Windows 7.
In your case with two HD's I'd unplug the Windows 7 Dual Booted HD to install Fedora, set first to boot in BIOS.
After install, plug back in Windows 7 HD, set preferred HD as first to boot in BIOS, boot other OS HD using one-time BIOS Boot Menu key.