the pro and free version are complete separate form each other and so have own databases if you buy the pro from the store.
But after installing the pro version you can copy the "database.sqlite" with iTunes on your computer (Device -> Apps -> Scroll to the bottom) from the free version to the pro version. So all your downloaded caches, waypoints and so on are copied.
After copying the database you have to authorize your account with geocaching.com in the configuration again. The other settings in the configuration are lost, but I think this can be reset in a short time.