Here is more from Chapter 12 of Up From Dragons (Skoyles and Sagan):

"Action Extension
Our brain is so flexible it actually allows us to experience ourselves in the artifacts we use. A surgeon feels extended to the tip of her scalpel. An operator handling radioactive material using remote-controlled “hands” feels embodied in his robotic arms. Perhaps when seated behind a steering wheel you have felt a physical sensation, a kind of wince centered in your head or in your spine, in anticipation of an automobile scrape; we have. Such body extension occurs even with phantoms. Among those who have lost legs, some feel the phantom – even if it has shortened into a stump – extend into an artificial leg (Riddoch 1941: 199-200; Simmel 1956: 644; Mitchell 1872/1965: 352). Some people with such phantoms embodying their artificial legs even report being able to feel coins or the shape of the ground underfoot. They not only feel it but can incorporate feedback from it into their motor control. The there is the Neilson illusion (Neilson 1963; Ramachandran and Blakeslee 1999). You put your hand in a conjurer’s trick box that contains a window through which you can “see” your hand. Of course, it is not your hand that you see but, through the clever use of optics, the hand of someone else hidden by a screen. The surprising thing is that you embody what you see, even when you attempt to move “your” hand and find that the hand that you are looking at remains motionless. Logically, you should realize that what you see is not your own hand. But instead, you experience a feeling that your arm is paralyzed. You have embodied yourself into the visual feedback generated by the sight of a stranger’s arm.

A variation of this phenomenon can be evoked using mirrors so that you see your right hand when you think you see the left one (or vice versa). That is not very interesting if you have two arms, but the effect can be enormously beneficial for those with a phantom arm. Recall that many phantom limbs are painful because the arm is in a twisted or impossible posture and so suffers “clenching spasms.” Shown their “real” arm in a mirror, people felt their phantom being touched when they saw “it” being touched. Some who had never been able to move their phantom found that they could, with visual feedback from the mirror. Some experienced a paradoxical effect in which the sight of their “lost” arm caused them to lose their phantom sensation, as if their brain needed them to see the missing limb as real in order to reorganize itself to let it “disappear (Ramachandran, Rogers, Ramachandran 1996; Ramachandran, Blakesee 1999).”

Why should this be so? The reason is that our brain’s experience of existing in our body does not arise from our body’s consisting of pieces of attached anatomy but through our brain’s ability to do things with them. This results in a “body schema” built up using the daily feedback from our body. As noted, people may feel a phantom leg existing, but only in the parts of it that move. (The internal organs – bladder, womb, and rectum – in which we can have phantoms might be thought to be exceptions, but they are muscled, even if it is only to let us empty them.) People are more likely to feel phantoms of the parts of the body that stick out. The sensation of a phantom breast or nose often will exist only at its tip, where there is most physical contact (Riddoch 1941: 207; Melzack 1990). We may not be able to move these parts, but our brains need to know they are there so that they can avoid bumping them.

Embodiment, therefore, does not directly map that which lets us move – bones, sinews, and joints. Instead it arises from the activity of populations of neurons distributed throughout the brain, using feedback that guides our movements in the external world. This is logical from the brain’s point of view, since the brain has no direct knowledge of exactly what our bodies are made of. The brain is very knowledgeable, however from sensory feedback, about the ability of its bones, sinews, and joints to change position, articulate, do things.

The part of our brain that guides the motion of our bodies is called the motor cortex, but it might more properly be called the “motor-control-under-tactile-supervision cortex.” As the neurologist Edward Evarts makes clear, injuries to the primary motor cortex particularly affect those movements made under guidance by somatosensory inputs (Evarts 1987).” Supporting this link is the fact that brain scans of people discriminating by feel with the right hand the length of objects (but not their shape) show that they activate their primary motor but not their somatosensory cortex. Oddly, it is the motor cortex of the right and not the left hemisphere that controls the right hand (Kawashima, Roland, O’Sullivan 1994). Our primary motor cortex is thus also a “somatosensory cortex.” The premotor cortex (found in front of the primary motor cortex) is likewise not a motor cortex but one that guides and organizes movement under visual and other sensory feedback (Flament, Onstott, Fu, Ebner, 1993; Grazino, Yap, Gross 1994). Neurons in the F5 area of the premotor cortex in monkeys discharge both when a monkey performs a hand action and also when one sees the same action done by another (Rizzolatti Fadiga, Galese, Fogassi 1996). PET imaging detects activation in the caudal part of the left inferior frontal gyrus of the motor cortex when people look at hand actions. It thus processes not only feedback about its own limbs but also that of others.

The supplementary motor cortex, another part of the motor cortex, guides our movements using inner scripts and plans (Goldberg 1985; Tanji, Shima 1994). Further, there is no sharp division in the brain between the cortex which receives sensory input from our bodies and that which sends motor signals; they are all part of a common process, differing only in degree of specialization. The somatosensory cortex, which is usually seen as the cortex that receives touch input, also has, for instance, its own projections to motor neurons in the spinal cord (Galea, Darian-Smith 1994). These projections are functional: Cool the motor cortex and the sensory cortex can take over the control of movement (Sasaki, Gemba 1984). Our sense of touch is, therefore, intimately bound up with motor control in both the somatosensory and primary motor cortices.

What is conspicuous by its absence in the brain is anything like a “muscle cortex” (Schieber 1990). No cortical neurons have been found that act upon individual muscles in the way piano keys activate the movement of piano strings. Instead, all motor neurons in some way map what can be done through the muscles (Scheiber, Hibbard 1993). Thus, it is through our doing things with our body that we get a sense of being in a body."

So, there is no 'anatomy book' in the brain. It couldn't care less which muscles we use to do things with. It is up to us to learn to "feel" our bodies as we do things, to practice sensing ourselves doing things, so that we can keep our brains/awareness informed about its own output, our bodies out of pain.

If we consider the body as not at all separate from our brains, but rather our body parts as simple extensions of brains, this should help quite a bit. ("The body as the 'blob on the bottom of the brain', rather than the brain as 'the blob at the top of the body'.")

Our sensory input systems aren't there to plague us with annoying discomfort, instead they are there to help guide our activity so that we don't sit in the same position for hours on end. (Even if the prefrontals are having a good time thinking, other parts of the brain are likely getting very bored from the lack of stimulation.) In fact, sensory input is so completely integrated into the motor output side of the equation, that it isn't possible to move a hand even a slight amount without your brain sensing that movement, and in many places, even on the ipsilateral side of the brain, being able to adjust that movement.