You do want to figure out how to mount and unmount those CD-ROM Drives. Use the link FancyPiper gave. As far as shutting down, I've had luck with both shutdown now and poweroff. I mostly shutdown from konsole now with poweroff more than any other method because it's quicker, especially from X-KDE!
Had a few issues with shutdown now here & there. You can use these commands with all users, not just root!