Terá de editar /etc/fstab para o montar automaticamente durante a inicialização. Algo semelhante a:
Em terminal ...
sudo blkid # to obtain the correct UUID number
sudo mkdir /media/username/some_mountpoint_name # for drives owned by root
sudo chown username: /media/username/some_mountpoint_name # for drives owned by username
e adicione algo semelhante a um deles para /etc/fstab ...
Em terminal ...
gksudo gedit /etc/fstab
# shared EXT4 disk
UUID=correct_UUID_# /media/username/some_mountpoint_name EXT4 defaults 0 2
# shared ntfs disk
UUID=correct_UUID_# /media/username/some_mountpoint_name ntfs-3g defaults 0 0