The global version of EC-CUBE only supports plugins at this time. Is there any reason you do not want to build a plugin? Since the code is open source you are more then welcome to view the source code of our PayPal plug-in here:
We also have a plug-in tutorial guide in English that can be found here:
If you are using the Japanese version of EC-CUBE, it uses both modules and plugins. Functionality is the same, however the structure and installation is very different. Modules can not be installed manually and they require you to log in to your EC-CUBE official account to retrieve them.
Plug-ins on the other hand, can be installed manually and therefore do not require the EC-CUBE online store. If you plan to use the global version of EC-CUBE or you plan to distribute your app locally, a plug-in is probably the best way to go.
Let me know if you have any other questions.
Thank you again