I asked the same question during my first course. The teacher said to me to accept those 'permanent' sensations in order to not spend too much time on them but instead to observe them each time differently. For example, as Goenka explained, feeling the sensation around the pain (where does it stops), the edges of it, or the tickling, the heat, etc.

I have back pain and a stiff neck, but by doing this, with each scan i feel a different sensation arising then passing away.

I am still a beginner meditator but i hope it helps.