insert the server 2003 cd and boot from it.
during the installation when it prompts to select the drive for installation, select D:\ drive.
further,the installation prompts you with the option of weather you want to format d:\ or you want to leave the files intact. select the later one.
another option i would suggest is that to repartition one of your drives to create some free space and then install server 2003 on it.