The most critical point we should remember is that like oxidation state assignments, electron counting is a formalism and does not necessarily reflect the distribution of electrons in the molecule. However, these formalisms are very useful to us, and both will give us the same final answer.
Consider the following simple examples. Notice how some ligands donate the same number of electrons no matter which formalism we choose, while the number of d-electrons and donation of the other ligands can differ. All we have to do is remember to be consistent and it will work out for us.