All your personal files go somewhere into your home directory. If you want to find them reasonably efficiently, when you need them, you need to put in some effort into keeping your files organised well. This sounds like a bother, but most of the work is slight, after an initial planning phase. During the planning phase, you decide where each type of thing should be, and after that, you just need to put them there.
It's not very important how you organise things, as long as you know where to put everything, and where to find them again. Being systematic really pays off here.
Here's a few things to consider:
You may want to separate important data from scratch data, to avoid backing up large files that have little value. If you put the scratch data into
~/scratchor a similar place, you can just avoid backing that up.
It may be worthwhile to separate active projects from inactive ones, or from archived files in general. You might have a
~/Archivedirectory into which you put files and projects that are no longer actively needed, but that you want to keep around.
You may also want to keep work and personal files separate, if you use the same computer for both work and personal stuff. You might even want to have separate logins for the two, to maintain a better work/life balance.
Related files probably should go together. For example, the program source code, text documents, video files, and audio recordings that are part of a game development project, probably should all go under
~/my-best-game-ever, rather than split up between
~/Documents, and so on.
Your source code checkout for a project should probably not be the top project directory. For example,
~/my-best-game-evershould not be a git working directory. Instead, that should go into
~/my-best-game-ever/src, or other name you prefer). Invariably, you end up producing things that are not under source control, such as release tarballs, photographs from release parties, or other such files. Then you put them under
~/my-best-game-ever/Releases. If you build Debian packages, those go into the parent of the source directory, so they'd go under
~/my-best-game-everas well, rather than into your home directory.
Why not take a look at your home directory, think about what sorts of content you have in there and then consider what organisation of files would work best for you? Perhaps you're already well organised, but maybe there's an opportunity for you to improve your computing life just a little bit.