In *NIX systems you have to manually add file systm into root filesystem hierarchy. Mount command used to attach file system found on other device like usb, cd, partition into root fileststem (/).
If you are using graphic then system automatically mount mdedia but if you are using command line then you have to manually mount media on their mount point.
When you shutdown system all mounted filesystems will be unmount.
when ever i shutdown in linux, i am using ubuntu it says my drive didn't unmount on shutdown and it might damage my files?
Where you get this message?