Making working relationships work is largely a matter of getting the parties involved to feel empowered and respected, and working toward a common goal.
The chain of command provides a clear line of responsibility from the executive suite on down. As part of the structure, you need to give employees a procedure to move up the chain if their concerns are not resolved.
Every aspect of your operation needs to be structured and documented so the results are predictable and the knowledge needed to execute is captured, clear, and transferrable. Systems should be created to provide repeatable results; rinse and repeat is the key.