Roof Modelling

Currently modelling a building where my ground floor has rooms at three different heights -> staircase finishes at 12m (floor height) and a gym finishes at 7m and finally my offices/toilets/circulation which finishes at 3.6m. My first floor finishes 7.2m.

I've tried to create two separate flat roofs. The first floor flat roof at 7.2m and a ground floor flat roof which says it starts at 7.5m. The ground floor flat roof consists of 2 sections both drawn from a 3D tool where one starts at the staircase 12m height and the other starts at the gym 7m height. At roof setup the model says ground floor (roof at 7.5m). I get a ton of warning messages after I try to apply this. 
Is it possible to alter this function to allow multiple roofs at different heights to be made to a single floor. Instead of one roof per floor?

Warning Messages.

Both roof sections shown are from a ground floor room (Sports hall and Staircase and finish at different heights)

Roof Setup