Probably best to explain how disks actually work in UNIX first.
You don't get drive letters in UNIX, drives become special files under /dev/. If you had a disk with three partitions in it, you would get something like
/dev/sda -- the raw disk itself, with the contents of all three partitions. This is the device you use when editing partitions.
/dev/sda1,2,3 -- The partitions inside /dev/sda. These are the things you format and mount.
To partition a disk in Linux, you'd probably prefer the commandline parted tool since it's common, supports several partition types, can do things like moving and resizing of partitions, and has a somewhat verbose built-in help. If you don't have it, you can try fdisk on systems with old-fashioned boot labels, but its abilities are more limited, and you must read its options carefully.
When you mount a disk, it doesn't become a drive letter, it takes over a folder, typically an empty folder. Say you had a folder /mnt/disk inside your root partition, you could do mount /dev/sda1 /mnt/disk to have its contents made available inside /mnt/disk. The root partition itself is mounted by the kernel on boot, because it has to start somewhere. You unmount partitions with umount /dev/sda1 or umount /path/to/folder , but can't do that to a partition that's in use.
Automounting of non-removable disks is typically done through /etc/fstab, a text file containing a list of partitions and where they belong. When the system boots, it will attempt to mount anything in this list lacking the 'noauto' option. If any fail to mount, this is considered a severe error. Here's a fstab from one of my systems:
# /etc/fstab: static file system information.
#
# noatime turns off atimes for increased performance (atimes normally aren't
# needed; notail increases performance of ReiserFS (at the expense of storage
# efficiency). It's safe to drop the noatime options if you want and to
# switch between notail / tail freely.
#
# The root filesystem should have a pass number of either 0 or 1.
# All other filesystems should have a pass number of 0 or greater than 1.
#
# See the manpage fstab(5) for more information.
#
# <fs> <mountpoint> <type> <opts> <dump/pass>
/dev/sda1 /boot ext2 noauto,noatime 1 2
/dev/sda3 / ext3 noatime 0 1
/dev/sda2 none swap sw 0 0
/dev/sda5 /home ext3 noatime 0 1
/dev/sda6 /usr ext3 noatime 0 1
/dev/sda7 /var ext3 noatime 0 1
/dev/sda8 /var/tmp xfs noatime 0 1
/dev/cdrom2 /mnt/cdrom udf,iso9660 noauto,ro,user 0 0
/dev/sdb4 /opt xfs noatime 0 0
# glibc 2.2 and above expects tmpfs to be mounted at /dev/shm for
# POSIX shared memory (shm_open, shm_unlink).
# (tmpfs is a dynamically expandable/shrinkable ramdisk, and will
# use almost no memory if not populated with files)
shm /dev/shm tmpfs nodev,nosuid,noexec 0 0
Once you've partitioned a disk, you format it with the mkfs command. There's actually many different mkfs commands, since there's many different partition types, but they have a lot in common and can be mostly used the same way. For example:
mkfs.ext4 -L volume-label /dev/sda1
would reformat /dev/sda1 with the ext4 filesystem. Other common Linux filesystems include ext3 and reiserfs.
Encrypting a disk isn't something I've tried personally. There seem to be quite a lot of steps involved, it's not a single command.