If you are a student willing to have a Java programming career, it might help to learn how to do things from command line, e.g. edit the files, compiling the classes, testing and building the project. Oracle tutorials provide example on this matter: https://docs.oracle.com/javase/tutorial/getStarted/cupojava/win32.html#win32-2
However, I strongly advise you to embrace an IDE as your Java career will mostly reside in an IDE as real life projects are BIG! There are tons of helpful things the IDE does to you out of the box or to simplify things. Since you are a student, I will give you one basic example besides compiling: a class with 10 fields requires you some typing for getters, setters, hashCode, equals. Alternative? Few keystrokes to instruct the IDE to generate them for you. And that's one basic example.
Regarding the project structure, embracing the (since you mentioned it) Maven project structure of src/main/{java,resources}, src/test/{java,resources}
even if you do NOT use Maven. This will let you forget about organizing the files around.
If you were asking about structuring the classes in the right packages, you will figure out yourself as you gain experience. Rule of thumb is to group classes together by functionality they provide. Additionally, if the packages are organized right, if you change something and touching a few classes, ideally you'd want the changed classes to be located in a single package if possible.
Learning Maven is a good choice as it is a powerful tool for building a project and keeping things organized (project structure, project dependencies, etc.).