Get you a sturdy 5 gallon plastic pail and place it upside down under the second floor bathroom. Now sit there and look up at the floor joists and framing. Picture where the toilet is going to be because that's where you are going to start your rough. Everything depends on the highest toilet in the house. Sit there for a good hour and plan, maybe even two hours. Then go upstairs and start marking it out. Of course, the big issue here is that you are just an apprentice and have no business doing anything other than drilling holes where your master tells you too. This is all stuff you learn from your master. You are not expected to lay out or plan anything except for maybe where to get my coffee from.