Sorry for the delay in response Robak.
I am assuming you are referring to Direct Fire Deviation of HE rounds... So to start...
I understand that with miniature buildings it is hard to impossible to get the miniatures in the building. There are ways to handle this. You can use an area on a sheet of paper (square drawn on the paper) and place the minis on this that are in the building. You can also lean the minis against the building. There are probably other ways to handle this as well...
As to stands taking damage in the building, well, per the rules, a stand is given hard cover unless the stand is in a Soft Structure which would give the stand(s) Soft Cover. This info is located in Chapter 15 Structures.
As to Direct Fire Deviation of HE rounds... If the round does deviate and still hits the same building then some one is lucky, but it can happen. The round probably just hits in a different location and the stands still gets the cover modifier. It may suck but it does happen.
I recommend you review the Structures Chapter as it pertains to the occupants.
Hope this helps!