ok. get partition magic. make two partitions with your windows. copy all of the 2003 server cd files onto the hdd (second partition). install server to the second partition. install it within windows. pick new install and make sure that you set it to copy all the files to the second partition
pick install to the G:\Windows folder (make windows folder in your secong partition) with g being considered your second partition (it might be a different letter on your computer). make sure that you check the "copy all of the installation files from the cd" option
boot into it when done installing. now right click your C drive and select format. it will delete it.
now reinstall server 2003 to the 1st partition exactly as above except everything is going to the C drive. when you are done, you can delete the second partition