Take a look at this project: https://github.com/sloria/cookiecutter-flask
It’s a great example for doing things the right way. Many of great Flask features are used: blueprints, application factories and more.
Here is how they register extensions, such as SQLAlchemy Database:
# app/extensions.py
from flask_sqlalchemy import SQLAlchemy
db = SQLAlchemy()
...
# app/app.py
from app.extensions import db
def create_app(config_object=ProdConfig):
app = Flask(__name__.split('.')[0])
app.config.from_object(config_object)
register_extensions(app)
...
def register_extensions(app):
db.init_app(app)
...