I trained for a marathon while doing P90x. I lifted heavy weights to combat muscle loss from all the miles I was logging. I did my runs on my cardio days. You will lose weight from running, but some of it will be muscle. I haven't started STS yet, but I can tell you that doing P90x while I was training for my race only helped me to maintain my current muscle mass. I did not lean out or gain any muscle. Also remember that the diet you consume for running will be different than the diet you use to build muscle mass.