By substitute teaching I'm assuming you must mean that you are in a long-term postion. I've done one in the past and I am about to start one for a 4th grade class this Monday to complete my last term of student teaching. So if that's the case the first point of order is to treat it as if it is your own classroom because it is until their teacher comes back. I know the class I will be taking over. They are an unruly bunch, not just for me, but for their regular teacher as well. I walked in on them and their sub yesterday and the room was in chaos. After I collected the materials I needed for the weekend I gave a short speech informing them that their teacher would not return until almost the very end of the school year. On Monday this will now be known as my classroom. On that day they will come to school and treat it just as if it was the first day of school. They will spend the first day learning what I want them to do and how I want it done, yada, yada, yada.
This really is the only way to get through this situation. If you don't you will spend too much time trying to learn how to do all the little things the way the regular teacher did them. It will result in too much chaos, wasted time, and frustration for you and the students.