The "upper" level concerns effects such as time and length differences observed when one object moves relative to another, particularly at speeds close to the speed of light. This effect was not suspected until Michaelson and Morley's experiments in the late 1800s which showed that light seemed to travel the same speed in all directions at all places of measurement, no matter what the location's relative velocity. It was assumed that the Earth moved through a medium called "ether" which conducted light waves as water conducts ocean waves. Light would travel the same speed in all directions only when the measuring device was at rest relative to the ether, and objects moving relative to each other couldn't all be at rest relative to the ether. This was then, and is still to some extent, a major scientific paradox. We can talk about it intellectually, and use "Occam's Razor" to try to find the simplest explanations for the puzzle. But "common sense" continues to try to tell us that "M & M", and all experimenters who since verified their findings, were wrong.
The more we investigate relativity and quantum physics, the more complicated the situation seems to become. It seems like we are making some wrong assumptions, rather like early astronomers who tried to explain the movements of the planets while assuming that they moved in circles with Earth at their center.
Perhaps a better way to deal with this is to examine the relationship between the two levels. The "lower level" is acceptable to Newtonian physics, and "common sense".
Wave phenomena in general exhibit a "Doppler shift". The usual example is the whistle of a moving train heard by a person standing along the tracks. It has a higher frequency as the train moves toward us and lower frequency as it moves past and away from us. Another example, a plane is traveling half the speed of sound, at a low altitude. There are two explosions on the plane, six seconds apart. A person ahead of the plane hears the explosions three seconds apart. A person behind hears them nine seconds apart. If they can both use a faster form of information transmission and see the explosions, they'll be able to understand their conflicting aural observations.
Since we know of no medium faster than light transmission, we have difficulty interpreting some light measurements.
We can still claim that Earth is the center of the universe. In our solar system, the sun may have most of the mass, and thereby the major influence on planetary orbits, but I (we) am the center of my consciousness, awareness and observations. I can see equally well in all directions throughout the universe. Also, the "world" (my environment at the moment) is not round, but mainly flat rectangular surfaces, usually joined at right angles.
Cosmology and quantum physics are to science what theology is to religion. They are both mainly exercises in logic and a means of impressing the public to get money. In this they are of some value as long as we recognize them as such. Belief in the big bang is perhaps a little better supported than belief in a conventional God. What kind of quarks make a proton is like how many angels can dance on the head of a pin.
What we don't know about the universe is probably infinite. The number of logical steps, all subject to question, needed to go from "common sense" everyday science to some of the "facts" of modern science approaches infinity. Therefore the probability of the "facts" being even close to correct is small. Of course the argument for God is even worse. But the truth of the big bang is much less pertinent to my life than the meaning of "God".
Actually, if I was to find convincing evidence that there was a God (not subject to explanation or the laws of cause and effect) that answered prayers and controlled our lives, I would probably start to enjoy taking risks to the point of suicide, because the physical universe would no longer have meaning. Even Hell would seem to be closer to the "real" reality.