Hi
We use Trello as a small project manager. We use the free version, because we are not a big company and mainly really in freelancer all over the world when we need extra services.
Basically we have a simple 4 columns approach. "Ideas","Approved/To be done", " in progress", "Done".
It's great because we can assign tasks, do multi lists and the system records everything that as to do with the boring stuff, like dates of assignments, deadlines, etc...
But first of all we do a first meeting, to define all the rules we will use, and "break apart" the "big" project to small parts.
We use HTML/CSS/JavaScript and Drupal mainly... when we need something specific we "freelance it"...
That's something we learn in the university. When you have a big problem, just break it in small ones. Solve all the small ones and the big one is over. :)