If you are able to boot into your computer, back up your vital documents and insert the Windows bootable into your DVD drive, and when the setup screen comes on, choose upgrade. This option is always there as long as the version you want to install is the same as the one you are currently using or higher.
If you are unable to boot into your windows to manually make a backup of those documents, do not worry. Insert the bootable windows XP, Vista or 7 into the DVD drive and boot from the disc, the computer will load the required system files first before prompting you on the type of installation. For Vista and 7, choose Upgrade, but if this option is unavailable then choose Custom and specify that it should leave your documents and folders untouched (you will see fresh installation and this option). For Windows XP, press Enter to install, choose the partition you want to install the Windows in and press Enter. In the next screen, you will see Leave the partition's folders and files (not exact words but very similar) and Format this partition. Choose the former and continue.
After installation your documents and files will be intact, but you might need to claim ownership of the former user's folder to be able to access the documents in the Deskop, Music, Documents, Downloads and Video folders (this will happen if you have passworded your former user account, if you need special assistance in doing this ask in the comment).
Now, if you were not allowed to install a fresh Windows without formatting and you need to get out your valuable documents, do not worry. Just boot from a linux CD ( http://linuxforpro.blogspot.com/2009/08/live-booting-linux-from-cd-rom-dvd-rom.html ) and copy out all your valuable documents or even your entire hard disk. Then you can do the fresh Windows installation.
For any extra help, feel free to comment.