Hi willmacdonald,
Yes, add CrashPlan to Espionage's whitelist. Also, sometimes backup programs use tiny helper programs to do the actual work, so you may still get prompted to unlock a folder, in which case you should use the prompt to whitelist the helper program (hopefully it will have "crashplan" in its name if such a program exists).
To backup the non-encrypted data, the folders will have to be unlocked. Then, choose Settings > Backup, and then click the "Change Selection..." button. You'll see a list of folders, and at the top-most level, alongside your hard drive, you'll see the names of the unlocked folders. Check the checkbox to back up these folders, and the folder contents will be backed up unencrypted (but, like all files, encrypted by CrashPlan's service).
You can also have CrashPlan backup the encrypted folders as well. Usually telling CrashPlan to backup your home folder will have it automatically do this, so long as your encrypted folders are located inside of your home folder (which they usually are).
Hope that helps! :-)