Waste pipes go down, and vent pipes go up through the roof.
Has your contractor "pulled" a permit for this job yet? And where has he posted his permit?
Have you checked to see if you have enough clearance around your plumbing fixtures?
A toilet of lav needs a 30" space.
Here is a typical drawing of two bathrooms stacked.
Here is a nice link to Bert Polk's plumbing tips