The 4% of all that is then, is the 4% that we are able to perceive with our 5 senses. Our theories on the 96% are based not of our perception of the 96%, but of its affect on the 4% we can perceive.
As pointed out above by Tangle, we don't really perceive most of the 4%. Our understanding of it is based on its effects on the infinitesimal fraction of reality we do perceive. There are indeed different senses perceiving different parts of reality - there are animals which can directly sense changes in magnetic or electrical fields that we can't; there are animals that can see wavelengths of light that we can't, there are animals that can detect all manner of chemical traces that we can't. All of this stuff would be within the 4%, though - that's how we're able to understand it.
Incidentally, does anyone know where this 96% figure comes from? Take dark energy, for instance. My understanding (which may well be wrong) is that dark energy is, in essence, the thing which accounts for the lambda term in the field equations of general relativity. We don't know what that thing is, but without that term the equations don't give answers that match observation. So we call whatever causes it 'dark energy' as a shorthand.
What does it mean, then to say that dark energy makes up two-thirds of the universe?