I just setup two backup drives for time machine in two different ways:
1) By clicking the "encrypted" checkbox in the time machine dialogue. After fininshing the backup, it spent a long time saying "encrypting..."
2) By formatting the drive as HFS+,Journalled,Encrypted using Disk Utility, and then keeping the the encrypted checkbox on in Time Machine (see note a).
The results are strange. The time machine preferences says that drive 2 is encrypted, however
diskutil cs list | egrep -i "size|status"
Size (Total): 1999702540288 B (2.0 TB) Size (Converted): -none-
The time machine preferences does not say that drive 1 is encrypted, though it too forever to do so. Perhaps that's because it's not mounted now.
(a) I also explored approach 2 while turning off the checkbox, thinking this would cause the material to be encrypted twice. However it said something indicating that it would decrypt the drive, so I stopped this.