I will assume that you do not know how to work GitHub and thus give a very basic idea of what it does. Adding files is very simple, to delete them click on them and a trash symbol will appear on the right of your screen. To create folders (knowing that GitHub will not have empty folders), you can click on create a file, type the name of your folder, and add a '/'. You will then have to create a small file just for the folder not to be empty.
If you wish to work on some part of code and you do not wish to modify the original, you can simply create a branch. That will copy the whole repository into a newly created branch, which you will be able to modify without influencing the original code. Once you are done, you will have to request a pull. That will allow everybody to see the exact differences between the original and the branch, such that we can see how yours is now different and if it's worth to change the original version.
I think that's it. Enjoy and have fun!
Felix