In order for configuration transfer to work for the very first time the target server must be empty very first time. You will create full export of the source and import it on target, doing this will make sure that the unique id of the portlets, pages match between source and target. After initial migration whenever you want to move content from source to target you can take the difference and import it in target
You dont have an option to install empty portal instead your suppose to install Admin portal first configure it and then run the empty-portal config task. Configuring empty portal is not allowed so fully configure portal before configuring it.
You can empty both Portal Server and express edition.
You have the option to turn a full Portal installation into an empty portal by running the ‘empty-portal' task.
< wp_profile_root >/ ConfigEngine/ConfigEngine.sh empty-portal
Important: When using virtual portals as production servers, you must create the virtual portals using the create-virtual-portal task; see Virtual portals reference for information. If you do not create the virtual portals using this task, the virtual portal instance is not empty and cannot be used to import a fresh release as a baseline.