There are several non-CD options for installing FC that you can invoke by booting from the CD and entering “linux askmethod” at the prompt.
The one I use a lot is the NFS install, because you can put the Anaconda installer update in the same folder as the CD iso’s and it will be used during the installation. Hard disk and various network options are also available. These are fairly well documented in the RHEL4 "Red Hat Enterprise Linux Installation Guide for the x86, Itanium and AMD64 Architectures" (see http://www.redhat.com/docs/manuals/enterprise/
If you do not reformat the partition containing your personal files, they will still be there after the update, but doing a backup beforehand would be a good idea. I have mixed experiences with reinstalling over a messed up copy of FC and prefer to wipe the partitions before reinstalling FC.
Your current situation is why a lot of people create a /home partition for their personal files. You would just leave /home untouched and reformat the other partitions. Another option would be to boot using a self-booting, live-CD version of linux like Knoppix (see http://www.knopper.net/knoppix/index-en.html
), mount the partition(s) and delete everything but your personal files. If you have never used Knoppix, it is a real eye opener.
Regarding apt, I really like apt as an installer and strongly encourage people to try it, but it does have a dark side, which is the removal of perfectly good packages during some “apt-get -f install ...” and during “apt-get -f dist-upgrade” calls. When used in the “apt-get upgrade” format, apt is fairly safe to use, but may not update everything on your system.
Unless I know of a good reason to allow apt to remove packages, I switch to yum to install any packages that apt has the removal issue with. For a fresh installation, I let “apt-get upgrade” do the initial work and then let “yum update” upgrade anything that is left over.