Upgrading to Catch Box Pro

I love CB public but decided to pay $29 and upgrade to CB Pro.  However upon uploading and activating, I see that alot of the standard customization is lost (example: menu setups missing, background image missing, etc).  I was hoping that all of this would not have been altered by installing the new theme. Ive set my theme back to public/free version until I get more comfortable.  Is there any kind of doc I can read that explains what I will need to re-do after activating the upgrade?