Hi Cosmos,
So the question is, what is silence and how do we make it an object of meditation? Can it be a thought? Even no-thing is a thought. It has to be if we are to favor it. But that is not silence. By definition, silence cannot be object, because it is the subject, the witness. It has no presence in time and space.
Now if we have some of that silence (witness), usually cultivated with an effective means of meditation, we can rest in it, and this has been proposed in the past as something to do mid-stream while we are in deep meditation. That is essentially the end of, or greatly reduced, cultivation of deeper silence, deeper witness. This was covered in several places in the lessons, including in this AYP Plus lesson:
Addition 79.3 - Favoring Stillness Instead of the Mantra During Deep Meditation? (Audio)
Jan 15, 2016
It is common for experienced meditators, and even sometimes beginners, to pick up the mantra once or twice and be gone in stillness for much or all of the session. That is normal and correct practice.
However, it is not correct to choose to not to pick up the mantra when we notice we are off it, even if we are deep in stillness, having blissful sensations, etc. Noticing we are off the mantra is the resumption of mental activity and what we do then is pick up the mantra and dive back in. Choosing to rest in stillness or sensations rather than picking up the mantra is a departure from correct practice and will lead to less results from our practice.
It is not we who decide if we are to be without the mantra or not. It is the cycles of transcendence and purification that determine that. When there is purification we experience thoughts and sensations, and when we notice, we take another dive with the mantra no matter where we are in the mind, even deep in stillness. This will take us deeper into stillness, cultivating abiding inner silence in a progressive manner, rather than remaining passively in a less deep level of stillness, which may be pleasant, but not as progressive a technique.
When we notice we are off the mantra we easily favor it at whatever level of refinement we are at in the mind. The mantra can be very faint and fuzzy and disappear almost immediately as soon as we pick it up. Then when we notice again later we have been off it, we favor it again. That is correct practice for our allotted time of sitting.
If it so happens that thoughts and sensations become so intense that we can’t pick the mantra back up, that is where Lesson 15 comes in. If there are no thoughts or sensations, and then we notice we are off the mantra (a thought!), then we pick the mantra up again. Very simple.
When we have a choice and favor resting in stillness or a pleasant vibration or sensation over favoring the mantra, this is not correct practice and will bring less results from our meditation session in daily activity. We don’t look for any particular experience, deep or shallow, when we are meditating. All experiences during meditation are part of the process of purification and opening. We just follow the simple procedure. Then we enjoy the resulting rising abiding inner silence in our daily activity during the day. Very simple and very effective for improving the quality of our life.
You will not regret favoring correct practice, continuing to cultivate abiding inner silence that will stay with you throughout the day and night. We can effortlessly relax in ecstatic bliss in rest time after deep meditation, at other times during the day, and all night while sleeping. Better to reserve our meditation session for the simple procedure of favoring the mantra. It is a small time to spend each day for greatly improving all the rest of our life experience.
Practice wisely, and enjoy!
Of course, this resting in stillness presumes there is some stillness that has been cultivated to rest in, and if so, it is not very progressive, as pointed out above. And in this case, stillness is not an object. It is a state of being, the subject, never able to be objectified. All attempts at that are outside of it, in mind. We can’t favor stillness. We can rest in it, but that is not advised during deep meditation as discussed above. Before or after meditation is fine. With correct practice, we will have plenty of stillness during the day, and we can rest in it any time we wish. It is our natural state of being.
Passive Awareness Technique
In AYP, for meditators who are sensitive to meditation with mantra, or breath, a technique called “passive awareness” is suggested, because it is very gentle and mildly progressive, least likely to create energy overload. See more on that here. Passive awareness is not meditation on stillness, because stillness cannot be object. It is “allowing” whatever is appearing in awareness, which helps to dissolve thoughts and sensations, eventually leaving stillness/subject with fewer or no objects. It is a style of meditation that works (Buddhist), and is gentle, which is why we suggest it for very sensitive meditators. But if mantra meditation works, best to go with that. Then stillness will be there for you. But you will not be able to meditate on it as object because it is not an object. Once you make it into an object, it is not stillness anymore. 
All the best!
The guru is in you.