You can deliberately use long breaths for a while if you want if you need to help the mind calm down.
Otherwise you just let the breathing happen naturally.
If you are doing a mahasi style noting technique then it might be approprate to label the breath as long or short. Otherwise just noticing whether it's relatively long or short is enough and you don't need to make a big thing out of the longness or shortness, it's just one aspect that you might notice.
Some teachers do encourage a progression of longness and shortness though, See Anapanasati by Buddhadasa Bhikku, or some of Ajahn Brahms explanations.
"Right effort is effort with wisdom. Because where there is wisdom, there is interest. The desire to know something is wisdom at work. Being mindful is not difficult. But it’s difficult to be continuously aware. For that you need right effort. But it does not require a great deal of energy. It’s relaxed perseverance in reminding yourself to be aware. When you are aware, wisdom unfolds naturally, and there is still more interest." - Sayadaw U Tejaniya