I have protected my application, but how do I really know it's protected by Code Virtualizer?

You can check if an application has already been protected by Code Virtualizer using the /checkprotected parameter via the command line. Example:

Virtualizer.exe /checkprotected MyApplication.exe

If the application is protected, it will exit with "Error Code = 0". If the application is not protected, it will exit with "Error Code = 1"

In that way, you can include in your build system that extra check, to know that your binaries have been protected as expected.