If you want to create a hyphenated port manage.py startmigration(see manage.py help startmigration), you must use manage.py schemamigration(as described in docs ), and you must do this individually in each application.
If you want to perform a migration (in other words, the actual database change, which I assume is true), the command for this is manage.py migratethat, if executed without any arguments, will transfer all your applications to the most recent migration.
There is only a script in my deployment manage.py migrate, and it works fine without manual intervention, regardless of how many applications have new migrations that need to be run.