Flask-SQLAlchemy's create_all() method will use the Base's metadata to create the table, by calling SQLAlchemy's MetaData.create_all() method. This method allows for a list of table objects to specify. You will also need to provide it a "bind", which is basically the engine. You can retrieve that using the engine property of Flask-SQLAlchemy.
So, you should be able to do...
db = SQLAlchemy(app)
class MyTable(db.Model):
...
class MyOtherTable(db.Model):
...
db.metadata.create_all(db.engine, tables=[
MyTable.__table__,
...
])
This assumes that you are using a single database. Otherwise you would need to do a create_all() call for each database using get_engine().