This is a pretty big debate that pops up continually on the main forums.
Should you, or should you not, eat back your exercise calories? The answer is: It depends.
Here are some background definitions before going into this:
BMR (Basal Metabolic Rate): The number of calories you burn at complete rest.
EAT (Exercise Associated Thermogenesis): Caloric requirements of training, or training expenditure.
NEAT (Non Exercise Activity Thermogenesis): Caloric requirements of activity that is not planned exercise. Vacuuming, driving, brushing your teeth, for example.
TEF/DIT (Thermic Effect of Feeding or Diet Induced Thermogenesis): Caloric expense of eating/digestion.TDEE: (Total Daily Energy Expenditure) = Sum of the above. BMR+EAT+NEAT+TEF
Exercise calories, as they are typically used in MFP specifically, is represented by EAT
in the above definition. Whether or not you should eat your EAT
(giggity) depends on what system or method you are using to calculate your intake needs.
If you are using most other online calculation tools to determine an intake estimate, that estimate is going to already include
EAT as part of the suggested intake. For example, it will ask you an activity factor that includes an average of your exercise, and with this it increases your TDEE to account for the fact that you are exercising.
If you are using MFP to tell you how much to eat, that estimate is NOT going to include EAT as part of the intake estimate. Myfitnesspal uses a caloric estimation tool that expects you to eat back calories burned during exercise.
Consequently, MFP will essentially give you a LOWER
intake estimate than an external TDEE calculator would give you.
In other words:
You tell MFP: I'd like to lose 1lb/week.
MFP says: Hey, you should eat X calories every day to lose 1lb/week.
You then decide to exercise and you burn 400 calories.
MFP says: Hey you pecker, you said you wanted to lose 1lb/week. Now you need to eat X+400 because you told me you wanted to lose 1lb/week.
So based on this: If you are using MFP to tell you how many calories to eat, you should probably be eating back some portion of your exercise calories.If you are using an external calculator and then customizing your intake to match that, you should not be eating back your exercise calories
Lastly: Exercise expenditure is often over-stated.
My general opinion is that it's much simpler and uses less guess-work to use a custom intake and just forget about the exercise calorie model entirely, but that's a different topic of sorts, more discussion of which can be found here: http://www.myfitnesspal.com/topics/show/819055-setting-your-calorie-and-macro-targets