Looking for guidance re large team designs

Still hope someone has a better way than bottom up design or naming conventions.

A simple example of the problem both Entity1 and Entity2 have internal NCOs. The NCOs are not visible at the entity ports. Each designer creates an NCO using the megawizzard and using the same entity name "NCO". Now we compile our Top which has an instance of Entity1 and an instance of Entity2. How to make sure each Entity (1 and 2) are built using the correct definition of NCO.

That is the problem -- solutions Naming conventions, bottom up design, or ??? Someone must know a better way.