I don't really have a source or website for counting calories or protein, etc. 11 or so years ago I started reading labels, paid attention to portion sizes, found a website that had a very basic list of all kinds of foods with macros, and printed that out. There were like 20 pages of single line, single spaced type. I still have it somewhere! I wrote down everything I ate in a journal. I also wrote down cals, protein, carbs, fats. It was very detailed. I did this every day for about 3 years.
I had goals when I started. I wanted to consume X number of calories, X grams of protein, X grams of fat, X grams of carbs. I was bulking and fighting hyperthyroidism at the time (though I wasn't aware then). When I hit my goal and kept hitting it every day for 2 weeks, I moved the goal up (still wasn't big enough). I got to the point where I was consistently consuming a minimum of 8,000 calories a day.
So after a while I just got to the point where I knew the macro breakdown of my most common foods. I knew how many grams of protein was in anything I ate. I could eyeball a portion size accurately if I had to (if I didn't already know it was a 12 oz. steak or 8 oz of chicken breast, etc.). Several years ago I stopped paying attention to anything but protein for the most part. Everything else to me is filler. I want protein, fats, veggies, and just enough carbs. Non workout days require less carbs, workout days I eat a little more carbs. I just kinda go by "feel" on carbs. Sure, I still plow through a few pizzas or potatoes or whatever, every so often. I'm not on a strict diet!
Anyway, if you count cals/pro/fat/carbs for a while, it becomes second nature and you don't really need fitday or livestrong or whatever at that point. Unless you're prepping for a show. If you've got a show coming up then everything counts.