Quote - my topic here is only to make a cover illustration for a evaluation study I have done. the study was hard work, and now I would like to finish the final report with a cover illustration, done by myself. just to show my creativity...
so everything in this project report is a product of my own and I don't have to use any third party image. a little bit crazy, I know, but it is my baby now... ;-))

I'm pretty sure I understand what you're trying to do, and the techniques I mention for molecules should apply, but with one one extra trick, that of using the scale dials to flatten the primitives, so you end up discs and lines.
You can then place the 2D building you mentioned on the discs using a 2D graphics app.

If I've misunderstood, a concept sketch or two might help focusing in on what techniques might help.