I'm don't know much about Fedora (I switched from RedHat to SuSE some time ago...) but I would imagine that during the install, you should disconnect your external hdd and let fedora install on your internal drive. I would check the
HCL to see if your hardware is supported (it may not have been added yet). Also check the RedHat site for advice.
Once you've got fedora up and running, try connecting your USB drive.
As I said, I'm by no means an expert, but hopefully this will help a bit