Mind operates by thinking and automatically. Can see this when let go of thinking .Is it the two layers of mind as superficial and deep?
If you're coming at this from the Yogacara or Zen schools, then absolutely. What you are experiencing is absolutely correct. There is the manas-vijnana or the thinking/superficial mind that sits on top of the klista-manas (or self-making consciousness) and the alaya vijnana or store house consciousness. The manas-vijnana is a street that runs both ways. While it is readily influenced by deeper consciousness, we can use the thinking mind or manas to influence the lower consciousness (this is called perfuming the seeds).
The real meat of Zen practice is the eradication the personal alaya and klista. This is done by suspending the manas vijnana through samadhi so we can access and work with the deeper layers of consciousness. When we suspend the thinking mind, the deeper layers begin to percolate up under their own energy. These thoughts will seem completely random to us - and, like you say, automatic - and can be comprised of memories, emotion, and some other really crazy stuff. The klista and the alaya speak a language that is different from the manas, and is instead common to dreams, myth, koans, etc. It is up to us to leverage emptiness, or mushin, to penetrate into what they represent, how they impact us, and their root causes. Bit by bit, we uproot these deep seated (seeded) causes of our ignorance and move closer and closer to enlightenment.
The nimitta is really just the mind experiencing the absence of the manas. It is marked by emptiness and a certain amount of stability. If it is unstable, there is something about your practice that is unstable. This could be anything from subtle volitions of the manas, movement of the body, any of the five hinderances, etc. What's troubling you is really a personal matter that is ultimately only discoverable through mindfulness. A teacher is your best option, but it may also be helpful to read some books on common meditation obstacles after you sit to see if anything resonates with your experiences on the cushion.
Can the mind watch the mind?
For example, try counting your breaths. If you lose count, your mind has wandered and your mind knows that it has wandered. That is the value of counting breaths. Counting breaths requires the mind. And mindfulness requires recall. Therefore, recall is the mind's test of mindfulness.
DN34:2.1.20: Furthermore, a mendicant is mindful. They have utmost mindfulness and alertness, and can remember and recall what was said and done long ago.
With practice, one might notice that recall can happen without thinking. So mind is more than thoughts.