There is nothing magical about this. Each of us is an individual, and our bodies transform food to energy with different efficiencies based on genetics, activity level, hormonal/endocrine changes, etc. We don't need to know the internals. You can treat the body as a black box, the internals of which are unknowable. However, you can measure certain characteristics: Input, in terms of how many calories you take in. State, in terms of measuring your weight accurately and frequently (daily). And, with less precision, a rough guess as to the amount of exercise. The last isn't even strictly necessary.
If you track your calories and weight for a month, keeping your activity level fairly consistent during that time, you can develop a sense for your own body's "transfer function". Once you know that, you're good to apply control to the process. It's true that the black box isn't time invarying, but over a reasonable observation interval, it's close enough. You can recalibrate this process as you go along.
Your body can't get or store energy from food it doesn't take in. If you're not losing, you need to either reduce the amount you're eating (no matter how uncomfortable that is), or increase your activity - without increasing the amount of food you eat to sustain it. Or both. There is no other way.