I doubt you can complete a Part 147 course without completing all the modules. If so, there is something wrong with the course/provider.
Anyway, when you come to apply you must send off your logbook with the required amount of experience and your module pass certificates.
Seems to me that you should also get a 'course completed' certificate from the Part 147 organisation, to allow the CAA to give you the reduced experience requirements.
Just what I've gathered from knowing a few Part 147 students, I'm a self starter.