1) You don't need to export (create a Jar file) the Source Java files to the SAP. You should use the Source Jar file
2) Any Java files change you should make in a new project folder that refers to the Default classes.
3) The new project folder is the project you should create a Jar file for and have the server refer to this file.
By create a Custom Jar file, you keep your changes together and they will not get mixed into defult files.