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Yes, all calories count. If you lift weights or walk or have any other activity, you will also have more calories burned.
Also by increasing your muscle mass you increase your resting metabolic rate.
Hope that makes sense!
Yes, some of it will be used to build muscle.
Calories are really just a loose measure, because different macronutrient components will be used for different functions in the body. For example, fatty acids might be used for repairing cell membranes, or they could be stored. Amino acids (protein) could be used for muscle, neurotransmitter synthesis, enzyme synthesis for chemical reactions, tissue repair, etc. All of these functions are part of the “energy burning” that requires calories.
This is why you need more calories, especially protein as your activity level increases because you need to maintain those basic functions and also build muscle.