If you are already running a kernel that is the same version of the one you are about to patch I recommend creating a fresh directory for the newly patched kernel. Remember that backups are never a bad thing. These are the files that I back up:
If you are not doing things The Debian Way you should also back up the /lib/modules directory, /boot/vmlinuz, /usr/src/linux/arch/i386/boot/bzImage and /usr/src/System.map. It's possible my notes on the location of these files differs. Do a locate <file> if they're not where I've stated they should be.