First of all I don't think there's a Fedora Enterprise, the title of the book is probably refering to Fedora AND Redhat Enterprise Linux. Most of what you've learnt in RH9 still applies to Fedora. They will still provide security updates for RH9 until April, however this doesn't mean you can't do your own research and make your own updates, and there's also the Fedora Legacy Project which aims to provide security and bugfix updates for Redhat end of life products.
More info here:
I'm not exactly sure whether you'll be able to upgrade from RH9 to Fedora, but I'd imagine you can, since I've heard ppl upgrading to Fedora just by using apt-get. The base layout of the 2 is very similar(if not the same), its just a matter of upgrading RPMs.
Yea Fedora does provide GUI configuration tools which were available in RH. However like any other distro, majority of them are designed to help you in doing basic configuration, if you want to fine tune your system and master Linux adminstration, you'll need to dig through config files yourself using the command line.