The following instructions are from Lama Zopa Rinpoche unless otherwise stated. A detailed account of these instructions is recorded in the Wheel of Great Compassion: the practice of the Prayer Wheel in Tibetan Buddhism.
Generating right motivation
Lama Zopa Rinpoche teaches that one should first generate the motivation of Bodhichitta, recalling when turning the prayer wheel:
The purpose of my life is not just to offer happiness for myself and to solve all of my own problems; it is to free the numberless other sentient beings. The purpose of my life is to be useful and beneficial for other sentient beings–that is, to free other sentient beings who are numberless. I will free each of them from all their sufferings and lead them to happiness in this life, happiness in future lives, perfect rebirths, the ultimate happiness of liberation from samsara, then the peerless happiness of full enlightenment.
Reciting mantra
Embodying the compassionate wish to benefit all beings, recite aloud the mantras inside the prayer wheel. One should resolve that by reciting mantras, one is doing so to actualize this intention for every being throughout the six realms.
Visualizing with prayer wheel
While spinning a prayer wheel clockwise, Lama Zopa Rinpoche teaches that one should visualize light rays emanating from the mantras, destroying “all the negative karmas and obscurations collected from beginningless rebirths.” In this way, the suffering and the causes of suffering of sentient beings are absorbed into the prayer wheel and destroyed there by the great force of wisdom and compassion. One should repeat this visualization several times, centering on all beings simultaneously or beings in the individual six realms. Visualize also that light rays are being sent out to all sentient beings throughout all the realms and universes, granting them happiness and well-being, and leading them along the stages and paths to ultimate enlightenment.
Dedicating the merit
One should always dedicate the merit to all sentient beings immediately after concluding any practice session. If you are in the habit of regularly using your prayer wheel, including during post-meditation sessions, make sure to periodically dedicate the merit. There are many great explanations on dedicating merit by the Great Lineage Masters. Venerable Khenpo Tsewang Dongyal Rinpoche often encourages us to dedicate merit just as Manjushri and Samantabhadra Bodhisattva. Lama Zopa Rinpoche provides the following dedication, perfect for any practice session:
By this virtue may I quickly attain the state of the Buddha of Compassion and lead all beings without exception to that enlightened state. May the supreme jewel, bodhicitta, that has not arisen, arise and grow; and may that which has arisen not diminish, but increase more and more. May the lives of those compassionate ones who’ve embodied in human form –His Holiness the Dalai Lama, the virtuous friends, and all holy beings–remain long and stable. As a result of these merits, by merely seeing, hearing, touching, talking with, or thinking of me, may any being be freed immediately from all sufferings, diseases, spirit harms, negative karma, disturbing thoughts, and all obscurations, and may they abide in the peerless happiness of full enlightenment forever.