Is File Vault 2 whole disk encryption or whole partition encryption?
John Siracusa's detailed Lion review covers the new FileVault disk encryption feature in great detail:

http://arstechnica.com/apple/reviews/2011/07/mac-os-x-10-7.ars/13#lion-file-system

To summarise, the new system is "volume" based. This means that not all volumes can be or are encrypted. The Lion recovery partition for example is not encrypted. Non Mac volumes are also not encrypted (FAT, NTFS, ExFAT, etc).

From John's description it does appear you can have multiple encrypted volumes. Whether or not they can use different passwords is unknown to me. Some use of the diskutil command may be necessary to achieve this if possible.