Regardless the format of the exchanged file and the type of the MEP applications in which it is opened, it is advisable to use the architectural model as an external reference.
In AutoCAD and AutoCAD MEP design environment, you should XREF the DWGs imported from ARCHICAD as opposed to merging them into the MEP design model.
See Working with XREFs.
For MEP engineers using Autodesk Revit, GRAPHISOFT offers the ARCHICAD Connection Add-In, available from GRAPHISOFT's website at:
http://www.graphisoft.com/support/archicad/downloads/interoperability/.
This add-in optimizes the IFC data import from any IFC data source to Revit used by MEP engineers.
It is recommended to create a project link between the imported architectural content and the MEP design to keep them separate.