Kei, I am not sure if you are referring to the "combine carbs and protein together" idea or the "seperate certain foods and eat them on their own" idea, but I did the latter as the first does not work with my stomach.
So, for example, I was eating tofu/other (mainly)protein food with veg and no (mainly)carbohydrate food, or perhaps (mainly carbohydrate) food like spelt pasta with veg and no (mainly)protein food, and then fruit just alone, like ginko said it may not need to be digested just to pass through and then if you eat it after other foods it can just ferment and cause acid and not digest sufficiently. And fats liuke avocados and nuts I could add to my meals. It worked well, I still mostly eat that way, its great for me. But to each body a different make up so I guess you need to try things and find out what works for you.