I did it manually when I wanted to be certain how many calories I was taking in. I started a food journal and listed each food item and quantity I ate. I used a few websites to find the nutritional information: calories, fat, carbs and protein.
nutritionix seems to be decent. It has been a few years since I did this, and the old sites aren't coming up when I search.
Google does a good job at presenting the info, or any of the first 5-7 google search return choices.
Important is to be honest with yourself on what, and how much, you are eating.
Whether with an app or manually, you will become familiar with how many calories are in the food items you eat.
Spend some time learning about your caloric requirements. Age, gender, activity level, all play roles. Good luck!
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