Reinstall W2K

Hi,
I believe that the os is corrupt and I want to reinstall W2k. I put the cd in and set bios to boot from atapi device first. It boots into W2K.
When I run from cd I have two options for install. One says it will upgrade (recommended)I am running W2K already and my existing settings and installed programs will not be changed. My question is this, will it leave all the documents and other things intact without deleting or removing? I could not run the recovery console because it would not boot from cd even though I set the bios to.
Thank you