When setting up the power meter on an indoor Elite Digital Mag Trainer should I put in my weight plus the weight of my bike when I input the weight?
Your weight is used for calculating your power to weight ratio (W/kg).
Weight of bike/clothes/other gear is not taken into consideration. It is considered that these things weight about the same for every "pro" cyclist. So you should use your own weight because everybody else is doing that. This way you can compare your results with your competition.