I did my first CCC backup earlier today and afterwards noticed that my applications folder is empty in my user directory on the new backup? I have applications selected for backup. Will it just not copy those?
Did you have anything in your ~/Applications folder on your internal drive, or only apps in your /Applications folder? Usually, apps are only installed in the /Applications folder, not under your user folder.
CCC can copy any part of your drive, or clone the entire drive, including OS, apps, documents, etc. Look at your backup settings and also look at the help feature. CCC documentation is very helpful and will guide you through properly setting up cloning.