How do you get all of the light switches to be in the down position for off when you have more than one switch for them?

Three way switches do not have a up-on down-off position. With the lights off, reposition the switches so that the handles are all down. This is the start position and depending on how you enter the room and turn on the lights certain switches will be left up when you leave the room. That is just the design of the switches and for the asthetics of the look, all handles down the lights will be out.