This tutorial explains how to use CrashPlan and FileVault together.
FileVault 2 on OS X 10.7 and later provides full disk encryption and no special action is required in order to use CrashPlan with File Vault 2. You can install CrashPlan via the default method (as root). CrashPlan is able to back up as long as an authorized user has entered his or her OS X account password to allow the system to boot.
There's a great article from CNET that explains how FileVault 2 works if you're interested in more details.
The default (root) user does not have access to File Vault-protected contents via Spotlight. This means Spotlight won't tell CrashPlan about files that have changed in the FileVault-protected account. If you are backing up an account that is protected with FileVault, you need to install CrashPlan to Run as User.