Accurate way to track workouts?

PresBC

Have been doing T25 Alpha for a full round, but am taking a break to get ready for a 5K I'm running in December. What I have been doing in the past is tracking my workouts with a HRM, then using this website to calculate over:

http://www.shapesense.com/fitness-exercise/calculators/heart-rate-based-calorie-burn-calculator.aspx

I copy my details into that calculator, then take the output and copy it into the Net v. Gross calorie calculator, and log whatever the outcome of that is. I have been doing this for T25, and I get higher than what would be considered normal calorie burns. I've attributed that to me being overweight and burning more to complete the exercises, but I wanted to see if anyone had anything to add. Today was my first day running, and my math says 506 calories burned, whereas Map My Run is telling me only 375. Am I doing something wrong, is there a better way, etc. Any response is appreciated, and thanks!