Both are RPM-based distros so you won't have many problems interchanging packages between them. I believe FC5 comes with Gnome as the default DM and Red Hat comes with KDE as the default. I'm not really sure if Red Hat comes with a package management system like pirut/pup in FC, but both distros should use apt-rpm as a means of updating and installing packages, although the FC community uses the yum command mainly.

Basically the big difference between Red Hat and FC is that Red Hat is targeted to the business sector and FC is targeted to the home user.