Supply lines are small, so they can usually run laterally through holes or notches in floor joists, but this isn't possible for 1 1/2" to 4" or larger drains. For standard dimensional joists, code forbids any joist notching in the middle 1/3 of span and allows you to remove only 1/6 of their depth in the other 2/3. You may not drill a hole any larger than 2 1/2" in a joist or any closer than 2 1/2" from the top or bottom. Thus, unless your waste lines can run parallel to the joists, you'll have to raise the floor, lower the ceiling or create a soffit below. Maybe someone else will chime in with ideas.