The following are some tips that should help you get the most out of using Axure on a large project:
Axure can promote, but not enforce, consistent design; ensuring a consistent design still requires a governance process
It is critical to construct wireframes properly and consistently across all teams
Create a naming convention for wireframes and dynamic panels; validate proper naming during governance reviews
Agree on a common structure/organization of wireframes and enforce that organization across all teams
Allow time to train new users on the finer points of using Axure
At the beginning of the project, pilot a number of ways for using masters and dynamic panels and then settle on a common approach; validate the implementation during governance reviews
Be sure to bake time into your project plan for maintenance of the Axure file
Refactor the project file at strategic points, such as before major usability tests, or before resuming work on the file following major de-scoping or major design modifications. Other refactoring effort may be required:
Between the completion of wireframes and writing the specifications
After the completion of a release
Plan on having one wireframe structure for prototypes and another for specifications