How do we perceive acceleration?
My question, Is it just visual perception or special mechanism for detection of acceleration?


Acceleration is a synthesized conclusion from a multitude of systems.

Most prominent is the Endolymph system you already mentioned:



As you accelerate, the endolympth and the otoliths within (small, calcified deposits) pass over the hair cells and produce action potentials which travel to the brain. The higher the magnitude of acceleration, the more action potentials will be sent.

This is also where dizziness comes from, as the endolymph and otoliths do not come to rest at the same rate, momentarily giving the brain two different interpretations of what acceleration you're experiencing.

There is also the Doppler Effect:



Based in the cochlear system of the inner ear this time, instead of the vestibular system, the doppler effect is interpreted by the brain and gives a very rough interpretation of both velocity and acceleration (if the velocity of the object happens to be changing).

Then there is the entire visual side of things. Motion blur and the speed at which the perception of objects change size are large contributors to our sense of visual acceleration, but almost all of this is done via complex manipulation of visual data in the occipital and frontal lobes.

There are also countless minor contributors: skin and join tension (the sensation of weight due to acceleration), ease of breathing, sensory cells in your hair if your hair is exposed to the open air while acceleration, blood pressure sensors (and numbness when the body can't compensate), etc.


  In any of these cases, why I was feeling more acceleration while siting opposite than in direction of acceleration?


My guess would be because your body is more visually attuned to facing the same direction as the acceleration, and when you were facing the opposing direction your mind overcompensated in an effort to protect you since you probably don't get a lot of opportunities to rapidly accelerate backwards over distances of more than a few feet.

Your brain might also have been panicking a bit because you couldn't see where you were going (usually very bad), and the heightened sensory state made the magnitude of the acceleration feel greater.

These are my best guesses, however. If someone has an academic source, please feel free to edit this answer!