When I did my track planning with SCARM, I found it to be both...bottom to bottom, top to top...it didn't matter. The key factor though is I still had to take into account the thickness of the underlying sub-roadbed plus the height of the roadbed material as well to get the total clearance needed. Different areas of the layout required different clearances, specifically where there was just a deck girder bridge I could get away with less distance between tracks. Where there was an elevation change in the landscape and/or there was a tunnel, I needed more clearance. YMMV.