gistfile1.py

# EngineをDB毎に用意
dsn1 = 'mysql://testuser:testpass@localhost/test'
engine1 = create_engine(dsn1, convert_unicode=True, echo=False)
dsn2 = 'mysql://testuser:testpass@localhost/test2'
engine2 = create_engine(dsn2, convert_unicode=True, echo=False)

Base = declarative_base()
db_session = scoped_session(sessionmaker(twophase=True))
Base.query = db_session.query_property()

# 〜〜〜 Entry, Commentテーブルの定義 〜〜〜〜 

db_session.configure(binds={  # <= どのテーブルがどのDBを利用するか設定
                     Entry: engine1,
                     Comment: engine2
                    })