"He who marches out of step hears another drum." ~ Ken Kesey
That's how we organize as well and seems to be the best option. I just automated it with a frontend in Filemaker so that instead of chasing a file down to email it you hit one button. Opening the directory is another button, etc. How about applying job info from your management program into films, and also press layout and scheduling? That was another of my petpeeves, manually typing job numbers into film seps.
We just started using Printavo. Could be pretty cool in the future but is really lacking many main features. Pretty much right now usefulness is limited to schedualing.