You should checkout the discord.py repository! It's well structured. https://github.com/Rapptz/discord.py

It's about what I'd expect from someone's first repository; not ideal, but a good start.

The general convention is to put the source code in its own subdirectory and have metadata files at the repository root. Your database should probably not be included in the repository as the scripts can generate it, so I'd remove it and add it to a .gitignore file so that it won't go to the Git history in the future.

In regards to your database code, it's a solid start, although relying on the garbage collector to close the database connection isn't really ideal. Instead, I would suggest you implement __enter__ and __exit__ methods, plus an extra close-method, to let the people using the database either use a context manager to handle the database connection or close the connection manually when they're done. An example use could look like:

db = Database()
with db('database.sqlite3') as conn:  # db.__enter__(...)
    conn.execute_query("SELECT * FROM records")
# implicit conn.__exit__()

The GUI code is actually pretty decent, although many of the comments feel redundant. Generally they should be used to tell why something is happening, not what, because the code already tells what it's doing, but it cannot tell why it was designed one way and not the other. Some of them could also be converted into docstrings.

Last, the README is empty. While not a problem for a project of this tiny scale, it should at least tell the name of the project and a short description.

I don't really have any simple project examples that use databases (the closest thing would be a certain server project, which is probably too complex for you right now), but to showcase project structure I can suggest python_ms.