One should ease into meditation by adjusting the posture using cushions and padded mats as necessary, rather than suffering insurmountable pain. We are interested in developing awareness and concentration, not a particular physical pose.
While the Buddha mentions four postures (sitting, standing, walking and lying down) it is the first that is the simplest to maintain for beginners. This sitting can be done on a chair or with the back against a wall, especially if this allows keeping a steady posture for longer sessions.
If you are flexible enough, the traditional seated postures (such as crossing the legs or kneeling) are definitely beneficial since they provide a stable triangular base. Flexibility can be built up over time through stretching exercises, yoga, and short periods in a traditional posture outside of a session.
If discomfort arises, treat it like other thoughts by noticing it, recognising that it is not your focus, and returning to the meditation focus. However, if it persists or becomes painful, rather than fidgeting, choose with awareness to move into another posture.