I have extracted everything from here. Pasted the important parts here incase the link goes dead.
Delete the partition table for the devices that will be used. This will delete everything on the selected device, so make sure that you have everything backed up on external media.
Create a new partition for the boot files.
The boot partition must be unencrypted for the system to boot.
No more than 256MB is needed for this partition and it can be kept on a usb drive for extra security.
The file system should be set to Ext4 and set the mount point “/boot”.
Since this is the boot partition, “Bootable flag” should be “on.”
Create another partition to be an encrypted volume for the swap space.
The size of this partition varies depending on the computer. Personally, I make it around 2xRAM.
Set “Use as” to “Physical for Encryption.”
Create a third partition for the root file system that should be around 6GB.
Select “Physical for Encryption” on this partition, also.
The last space that needs to be defined is the home partition which will be encrypted by Ubuntu and decrypted at user log in. This is where documents, pictures, music, desktop files and downloads are stored.
Make this partition any size that you’d like.
Personally, I use separate physical disks for my home folder and system files.
Choose “Ext4″ at the “Use as” prompt.
Set “Mount point: /home”.
With the partitions created, the swap and root volumes need to be configured:
Select “Configure encrypted volumes.”
Then “Create encrypted volumes.”
Highlight and select the volumes that are listed as “crypto” by pressing spacebar, then continue.
Enter a strong passphrase for each encrypted volume. This is the passphrase that you will be required before the system will mount the volumes and boot.
Finish and write changes
Each encrypted volume will now have space available inside of it. To configure these volumes, select the space listed under each encrypted volume.
Setup the first encrypted volume as swap space (choose this option under “Use as”).
The second encrypted volume, which was previously reserved for root system files, should be set to Ext4 and set the mount point to: “/”.
The final configuration should contain:
Encrypted volume > Swap space
Encrypted volume > Ext4, Root (“/”) volume
Unencrypted Ext4 Boot partition
Unencrypted Ext4 Home partition.
With everything setup, select “Finish partitioning and write changes to disk” and continue through the remaining installation prompts.
Create a username and password (different than encrypted disk passphrase)
When asked to “Encrypt your home directory”, select “Yes”.
This actually encrypts the user folder inside of the home directory but not the home partition itself.
The first time that the first user logs in to Ubuntu, a strong key is generated and can be recorded at that time. This is different than the passphrase(s) used for the root and swap partitions.
At the prompt regarding GRUB boot loader, select “yes” to install it on the master boot record, changing this could result in your system not booting.
After rebooting, Ubuntu will prompt for a preboot authentication passphrase that’s needed to unlock encrypted system disks. With this method there will be a prompt for the swap disk and one for the system disk, even if the passphrases are identical. In my experience, there will be an error on boot that says: “No video mode active”, this is caused by missing font files and is nothing to worry about it.