Always good practice to keep your Apps in one place, and your Data another. Personally what I do is set up another partition for data (and games) if on a laptop. On desktop, two physical drives at least. That way, the OS and Apps can happily reside on one partition - or disk - and Data on the other.
For backup many options exist. For quick, dirty and fully automatic, have your important data inside a Google Drive or Dropbox folder. Though for source-code, pushing to Github is better - assuming you do not mind your code being available for others to see and copy, or as Github is intended for, contribute to.
I took me some time to 'discover' Github as it were. At first it seemed a bit byzantine and, hmm, exposed. But once I got used to it, I can't really imagine any other way to store code. Version control is great - any change you do or blind alley you follow can always be undone easily when using Github. If stuck with anything, and need help, you can always include a little snippet of code in your help-post, and link to the github repo if anyone need see the complete context. It's there, and ready. Why not use it?
Also, for AppGameKit projects, you can always leave out pushing the media folder, so no-one can copy your project without at least putting in some effort - just edit the .gitignore file to include the line 'media/' and you're set. Probably a good idea to also add the line '*.exe' and similar for Mac or Linux depending on what OS you use so as to not push the executable to Github every time.
In other good news, working with Github is pretty much a required skill in any programming job, so if you got ambitions in that direction, might as well hop on board right away