For the proteins, only count the protein if it is from a good protein source. eggs, milk, meat, whey, etc. are good sources of protein. Nuts, oats, veg, etc. are not and should be ignored. In terms of carbs you don“t count fibre, and for fats you count them all good or bad. But remember that because you are disregarding some of these macros, as well as there are other calories in for example your cooking methods, you need to compensate for that. For example:
If I need 2000 kcals, I will first subtract 20% (depending on how clean I am eating), which leaves us with 1600 kcals. Then work out your Prot, Carbs, and Fats needs from the 1600 kcals.