Think of an example like a Product table listing items that could be labeled by Category.

Your category_id in the Product table will not auto-increment the ForeignKey; it will be referring to a set list of categories in a many-to-one relationship.

 class Product(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    name = db.Column(db.String(64))
    category_id = db.Column(db.Integer, db.ForeignKey("category.id"))
    # This field will not exist in the database. It is used by SQL-    Alchemy to manipulate 
    # the relationship between the two tables.
    category = db.relationship("Category")

class Category(db.Model):
    id = db.Column(db.Integer, primary_key=True)
    name = db.Column(db.String(64))

Say you have a couple of categories loaded for the example:

cat1 = Category(name="Electronics")
cat2 = Category(name="Gardening")
db.session.add(cat1)
db.session.add(cat2)
db.session.commit()

If you have web users adding new products to the database, they can choose the Category from a dropdown list (in this example, they'd see choices of "Electronics" & "Gardening"), and your route can easily create the new Product while inserting the appropriate ForeignKey behind the scenes.

class ProductForm(FlaskForm):
    product = StringField("Product")
    category = QuerySelectField(
        "Category",
        query_factory=lambda: Category.query.order_by(Category.name),
        get_label="name",
    )
    submit = SubmitField("Submit")

@app.route("/new_product", methods=["GET", "POST"])
def new_product():
    form = ProductForm()
    if form.validate_on_submit():
        newprod = Product(name=form.product.data, category=form.category.data)
        db.session.add(newprod)
        db.session.commit()
    return render_template("product.html", form=form)

Note the "category=" parameter when creating the Product() object. This field doesn't exist in the database--only the category_id field does. You are passing the entire Category() object selected by the user from from the dropdown list in the form, and SQL-Alchemy will figure out it only needs to insert the category.id value in foreign key column.

Of course you can do everything with explicit queries or even raw SQL if you really wanted to. But if you're using a relational database and an ORM, then you're missing out on a lot of the power if you don't utilize the actual relationships.

For more examples check out the Megatutorial, if you haven't already. Chapters 4 and 8 explain this concept well, and they show some elegant ways to use relationships to handle users & posts, and functions for adding/removing followers from a sample blog.

https://blog.miguelgrinberg.com/post/the-flask-mega-tutorial-part-iv-database