You want to meditate, you sit down, and after three minutes your back, knees or hips start to hurt. Your mind can't settle because your body is complaining. If that sounds familiar, you're not doing anything wrong. Usually it's simply a question of finding the right posture.
In Japanese culture, the way you sit is anything but a side issue. Before you work with the breath or a mantra, you sit, and how you sit decides whether your body carries you or distracts you. The character 坐 (za) means "to sit," and you'll find it in zazen and in many other words for practices that begin in stillness.

Sitting postures 坐法
There isn't one right posture, only the one that fits your body. What matters in all of them is a straight spine, relaxed shoulders and a slightly tucked chin. Everything else is adaptation.
Chair or stool. The most accessible posture, and not in the least less valuable. You sit toward the front edge so that your back is free, with both feet flat on the floor. In Japan, experienced practitioners also use stools when their knees need it.
Seiza. 正座 seiza, literally "correct sitting," is the classic Japanese kneeling posture on the heels. A cushion or a small seiza bench takes a lot of pressure off the knees.
Cross-legged. The legs are loosely crossed, ideally with the knees lower than the hips. A higher cushion helps to tilt the pelvis forward so that the spine stays upright without effort. For most practices this is perfectly sufficient.
Half lotus. One foot rests on the opposite thigh. It's more stable than sitting cross-legged and less demanding than the full lotus, and many people stay with it for life.
Full lotus. In the full lotus, kekka fuza 結跏趺坐, both feet rest on the opposite thighs. Pelvis and knees form a stable triangle. It's the posture in which Buddhas are depicted sitting on their lotus pedestal, the rengeza 蓮華座. Please don't force it, though. The hips often need years for this, and forcing it can hurt your knees.
Lying, standing, walking. Meditation isn't limited to sitting. Lying down can lead to deep relaxation, with the challenge of staying awake. Standing is common in qigong, and in walking meditation (kinhin 経行) each step is joined with the breath.

Hands and breath 息
There are a few simple hand positions anyone can use. You can rest your palms on your thighs, which many people find grounding. You can place both hands on the lower belly, on the tanden 丹田, which brings your attention to the center of the body. Or you can rest your hands in your lap in the meditation mudra hokkai jōin 法界定印, with the thumb tips gently touching, as you see in Zen and in the Womb Realm form of Dainichi Nyorai. The many other mudras of the Japanese traditions belong to initiation.
For the breath, it's enough at first to let it sink down into the belly rather than the chest, without forcing a rhythm. This calm belly breathing is a good foundation for breath meditations like the 108 Breath Meditation.
Common mistakes 注意
The most common mistake is sitting too low. When the knees are higher than the hips, the pelvis tilts back, the lower back rounds, and after ten minutes everything hurts. A higher cushion or a folded towel usually solves this. The second is tense shoulders, which tend to creep up toward the ears during meditation, so it's worth checking them now and then. The third is forcing the full lotus, which isn't a goal but one possibility among others. The depth of your practice doesn't depend on where your feet are. And finally there's wanting too much too soon. It's better to start with five minutes and slowly increase. As the Zen saying goes, 日日是好日, "every day is a good day," including the one on which you only managed three minutes.

More than ergonomics 道
Of course, posture is partly a practical question of sitting comfortably enough to stay still. In Shingon, however, the posture itself is already practice, because body, speech and mind belong together. The body becomes a vessel, the upright spine a channel, and the breath sinks into the tanden. In other words, when you sit upright and breathe calmly, your state already changes before any technique begins.
If you'd like to go further, have a look at the moon disc meditation, and if restlessness, doubt or boredom show up along the way, at the article on the nine resistances in meditation. Which posture works best for your body at the moment?
Your next step
Posture is the beginning. In Shingon Reiki it comes together with breath, sound and ritual. If you like, have a look at which entry fits you.
Your Path in Shingon Reiki The 108 Breath Meditation