WARNING: Extremely n00bish question lies ahead:

When I'm going to be updating my PC from Debian 5.0.5 w/ KDE, can I completely write over it and everything but the data of one folder with Debian 6 w/ GNOME? If I have to take the specific data off the computer, that's fine. I'm just wondering if I can change my GUI when I upgrade the OS.

Of course. The process it this: do a dist-upgrade (don't reinstall). When you're done, you'll have a 6.0 w/ KDE desktop. Then just use aptitude to install the gnome metapackage. Then you'll have to logout and select Gnome from the login manager. AFter that, if you want to get rid of KDE, you can just purge kde.

The only problem I have with doing it that way is that I am going to be installing Debian 6.0 (and Gnome) from a disc that comes with a book called The Debian 6 Bible. (and it's a laptop, not a desktop, though that shouldn't change anything.)

Then I would backup my data to an external drive and install with the disk, which will be Gnome based most likely, since that's what Debian defaults to. If the book includes a KDE version, you should just have to change the desktop during install. But like I said, Debian defaults to Gnome.

It is not a matter of installing KDE "over" Gnome. You install it along side of Gnome (and any other window manager you might have). Then, at login, you choose which desktop environment or window manager you wish to use.

It's all Linux underneath; all you are doing is changing the presentation.

Me, I favor Fluxbox, but I can switch to KDE or Gnome or even TWM if I wish to (I don't, but it's interesting for historical reasons).

They all coexist.

1. Like frankbell said they all coexist ,after all kde,gnome,fluxbox,icewm,jwm are programs(window managers) to make task easier, you can install them and remove them according to your needs, easiest way is of-course over network through software manager ,or from command line using aptitude, this way u dont have to worry about dependencies and updating x files manually.
2. As you said you want to take off some data off computer, easiest way is to use a rescue cd (puppy or knopix). and for future install mount your home directory to some different partition(say sda2) other than installing partition(say sda1), this way your valuable data remain safe if u want to install a new version or even other distribution all you have to do is install new system(say on sda1 or sda3) and mount sda2 as /home.