Hi Gregor
You may want to view a couple of older posts on this topic (there are so many posts now: it is hard to find them all but I dug this one out):
Frequency of Practice and Recovery Time.
The short answer is - yes, you can work the same area every day
if you want to. Think of braces for your teeth: these are worn every single day. Think of someone in the hospital lying in traction - it is every day. The yin tissues are not like the muscles. The muscles really do need time to recover from a strong workout, but not so for our connective tissues.
Of course, if you go too far and hurt yourself, then - yes, let that area rest and repair itself before you work it more.
You may choose to work different areas each day: that is fine too, but not necessary. It is just nice to have a variety and for other reasons, you may want to vary your practice. Think of working different meridian lines on different days. I don't always work my hips every day: one day I focus on my spine, the next day on my hips. It comes down to your intention.
The same answer applies to your second question: do we focus on the physiological effects (hips, spine, etc.) or the energetic effects (Liver, Kidneys, etc.) The postures may be identical for a Hip sequence and a Liver sequence but the intent is different. When your intention is to mobilize energy to the Liver, you will concentrate on the feelings of chi flowing and visualize the Liver becoming healthier. If your intention is to open the hips, you will focus on softening and allowing the hips to open.
Cheers
Bernie