Yes. What going to happen is the Mac OS X installation media disc will overwrite the existing partition on the HD by erasing it and will install a clean OS onto the partition. Whatever data was on the pre existing partition will be loss unless you have made a backup using CCC or Time Machine.
Just following the standard install path (which means not manually erasing the drive, as the installer will not offer you the option of a "clean install") will not delete any of your data, but will replace all system files. The Archive and Install option is gone, but the new install approach is closer to that, except that it doesn't save the old system files and folders. Just put the disk in and follow the prompts.