Brad
In the plans I'm having drawn up we are building up the floor 10 inches from the actual timbers!!
In any case I would think it would be better to drill into the top of any beams as the neutral plane is theoretically where the shear stress is!!!
I think in General the most important part is planning your house so that the plumbing is all in one section... i.e. superimposed bathrooms or bathrooms sharing a wall with the kitchen etc....
Carlos
