New encryption feature in Ubuntu 12.10: home encryption or full disk encryption? or both?

How do I correctly encrypt the entire partition when installing Ubuntu 12.10? I ask because the new Ubuntu installer now shows two encryption options.

After choosing "Encrypt the new Ubuntu installation for security", the "Encrypt my home folder" option is still offered later on. Do I need to check both options to have full encryption, or just the first option?

What will happen in each case?

Canonical implemented this feature (full disk encryption) in Ubuntu installer edition from 12.10 because Alternate CDs are dropped. From QQ Alternate CD are no longer available.

"Encrypting full disk" stands for creating encrypted volumes (luks) and it uses full disk, not only /home folder. Encrypting full disk is more secure and with that option you can uncheck "Encrypt my home folder". There is no need to use two kinds of encryption. If you want just to encrypting your home folder (without encrypted / and swap partition) use only the second option.