What works for me is continuous tracking. As long as you continuously track weight, body weight, activity (fitness monitors or the pedometer on your phone), and calories you will be able to make corrections based on the output (basically body weight with some corrections based on what you see in the mirror if you lift weights or exercise regularly). Even if your calorie estimations are off eventually for the day, it will show up in your body weight so you just adjust your estimates based on that to develop your "feel". Buying a food scale and cooking your own food really gives you a good feel for the calories involved with various ingredients. After a few cycles of calibration you will get a better at it and it will be less of a burden.
