clash detection and all traits in one model

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Respected Authority,
An office has given me a task to do 3D modeling of G+4 on Revit for architecture, structure and MEP. After that I am required to do estimation, integration of this estimated complete model in Nawisworks along with P6 schedule and do clash detection between different traits of the building, especially Structure and MEP. Then do energy analysis for the designed building. My concern is how to design a live model consisting of all traits on Revit i.e. architecture, structure and MEP. I have completed architecture and structure in one template and have to start MEP. I designed all Plumbing fixtures on the same model and placed them. But, when I am placing drains, they are all going on NGL, weather I place them on 1st or any other elevated floors.
after looking and reading online solutions, I linked my model in MEP template to do complete MEP but, this posed a new problem. the linked model is shown as an image and i can not hide or move anything in that model. means it is not a live model any more and i am unable to do any editing. this makes me think that how I will do clash detection between MEP and Structure? how i will deliver a single live model comprising of all traits i.e architecture, structure and MEP to client? need assistance.