We should breathe naturally. Don't concentrate on your breathing. Give all the attention to the mantra. A simple way might be to say the mantra as you breathe in, and breathe out in silence. Learning to breathe well, using the abdomen, is highly recommended for health not only for meditation.
Proper breathing is an important aid to relaxation and goes with posture.
Father John did not stress breathing, as he was concerned to keep the discipline simple and not to emphasise the method too much, because then that gets turned into technique. When you get too interested in technique, you forget the purpose of it. The most important rule of posture is to keep the spine upright. If you use a chair, find one of the right height that gives your back the kind of support it needs. If the spine is held erect and relaxed it is possible to stay alert.