This has been discussed extensively so I suggest you try exploring the archives.
There is not yet a single, ideal approach to this. It is on the wish list (somewhere, I hope it is not forgotten) but perhaps you should renew the subject with your absolute elevation reference idea. I don't recall if that has already been suggested or not.
The two common approaches are:
1. Hotlink the various buildings into the master file bringing all stories into common ground, 1st, 2nd, etc. stories. Then adjust the module elevations in 3D.
2. Save each building shell as an object and place on the site plan.
Each has pros & cons but they both work pretty well. The choice depends on how you work, what your hardware can handle and what you want to do with the master file; whether it is mainly for renderings and animations or will be used to produce detailed site plans and sections.