The body takes care of weight on its own if he operates as closly as possible to what he's "programmed" evolutionarilly (what it knows).
My experience is to first fix the lifestyle and diet. Regular movement and a low carb, natural (unprocessed) animal based diet is most consistent with our evolution.
Calorie restriction might be effective in the short term but not feasible long term as it need active mental strenght to overcome constant hunger feeling and cravings.
Lastly, calorie in vs. out is the wrong concept for many reasons. Not at least because the body does not know what a calorie is nor can in/out be realiably measured (the calories shown on the package are averages at best).
Hope that helps.