Along the lines of http://flask.pocoo.org/docs/patterns/mongokit/, I have a MONGODB_DATABASE setting, which is set to my normal database name. Then access the database via the connections' dictionary syntax, instead of attribute syntax (I have a helper method to make this prettier):

  connection[app.config['MONGODB_DATABASE']].mycollection.find_one()

The unittest code just modifies the setting:

  import unittest
  def setUp(self):
    myapp.app.config['MONGODB_DATABASE'] = 'test'
    self.app = myapp.app.test_client()

  def tearDown(self):
    # can clean up here, e.g.
    connection.test.drop_collection('mycollection')