You need to drive the layout process to a successful conclusion. When working with a CAD group, it is essential to spend the required time with the CAD personnel to explain the design including providing a description of the circuit, why it is essential to place certain components in the proper locations, defining the I/Os, outlining the power supply, and providing a complete board outline. After all, the CAD department is only going to do what they are told to do. It is the responsibility of the designer to communicate to them the desired layout and to maintain that communication until the desired result is obtained.