Carbon Copy Cloner and FileVault Volumes
I replied earlier with an answer without noticing you had tagged it as Lion related; take a look at this document, it should answer most of your questions.

From the Developer of CCC:

↘ link


  Is there any possibility to have the backup on my other second drive be encrypted?
  
  Yes, you can enable encryption on your backup volume, or reformat it
  as encrypted using Disk Utility:
  
  Full Disk Encryption (Lion only)
  
  CCC fully supports Lion's Full Disk Encryption.