app.py

from flask import Flask

app = Flask(__name__)

database.py

from application import app
from flask_sqlalchemy import SQLAlchemy

app.config['SQLALCHEMY_DATABASE_URI'] = 'sqlite:////tmp/test.db'
db = SQLAlchemy(app)

"""Only called if the application has never been initialized. Probably called from the python shell."""
def create_all():
  db.create_all()
  
def commit():
  db.session.commit()

file-structure.txt

/home/austin/your-workspace/
  your_flask_app/
    __init__.py
    database.py
    app.py
    user.py
  main.py

main.py

import database
from user import User

def add_some_users():
  admin = User('admin', 'admin@example.com')
  guest = User('guest', 'guest@example.com')
  admin.save()
  guest.save(guest)
  database.commit()

user.py

from database import db

class User(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    username = db.Column(db.String(80), unique=True)
    email = db.Column(db.String(120), unique=True)

    def __init__(self, username, email):
        self.username = username
        self.email = email

    def __repr__(self):
        return '<User %r>' % self.username
    
    def save():
        db.session.save(self)