• There you have the classic static/ and templates/ folders. The templates/ folder contains macros, error views and a common layout.
• views/ folder to separate the user and the website logic, which could be extended to the the admin views.
• The same goes for the forms/ folder, as the project grows it will be useful to split the WTForms code into separate files.
• The models.py script contains the SQLAlchemy code, for the while it only contains the logic for a users table.
• The toolbox/ folder is a personal choice, in it you keep all the other code the application will need.
• Management commands should be included in manage.py. Enter python manage.py -? to get a list of existing commands.
• Makefile for setup tasks, it can be quite useful once a project grows.

pip install virtualenv  
virtualenv venv  
venv/bin/activate (venv\scripts\activate on Windows)  
make install    
make dev  
python manage.py initdb  
python manage.py runserver  

Thanks to https://github.com/MaxHalford for his boilerplate Flask project.