At this time, Django defaults to MYISAM...but I wish to change it out to ensure that each time I produce a new table it's innodb.

Put that in configurations.py:

DATABASE_ENGINE = 'mysql'
DATABASE_OPTIONS = {"init_command": "SET storage_engine=INNODB"}

UPDATE

For Django >= 1.2 this ought to be write such as this:

DATABASES = {
             'default': {
                         'ENGINE': 'mysql',
                         'OPTIONS': {'init_command': 'SET storage_engine=INNODB'}
                        }
            }

See here