In his article, Miyaki expounded on the downside of cardio and why traditional cardio is poor for fat loss. The majority of your training should be anaerobic (strength training/interval training), as opposed to aerobic (traditional lengthy and low-level) in nature.
Attempting to alter your physique goes beyond simple calories in versus calories out. The key is to elevate your resting metabolic rate (via anaerobic work) to promote better post-workout fat burning and muscle building. And yes, diet is important here.