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.
“Peace is within oneself to be found in the same place as agitation and suffering. It is not found in a forest or on a hilltop, nor is it given by a teacher. Where you experience suffering, you can also find freedom from suffering. Trying to run away from suffering is actually to run toward it.” ― Ajahn Chah