This never really occurred to me until now, so maybe it does not categorize a really important question, but according to Quantum theory anything that "is not observed is probability until it is observed when it condenses down into matter." So with that said i would like to know if that theory has any any contradictions with atom theory. Atom theory is pretty straight forward but because you cannot see atoms on a macro or even a microscopic scale (only nano or smaller), how does that work with quantum physics. You cannot observe atoms with your eyes even if your looking at something with mass, so does that mean (supposedly) that atoms are only probability until you can observe them the proper equipment, even tho on a smaller scale thats what the things you are observing are made up of?
"To observe" is not the same concept as "to see". In physics "to observe" means that you have a concrete way to make a measurement on a given system and get back numbers (measures) out of it. It happens that these numbers are very well predicted by quantum theory. But atoms can also be seen directly as shown using some recent technologies that made possible very accurate analysis of materials. I think you should read this but you can also find very beautiful images on internet.
In Quantum theory "observation" means "interaction with the measuring instrument". This interaction (=observation) can made even without human if experimental data are collected automatically.
For example, let's consider an experiment when an electron goes through a screen with two small holes. Behind each hole we install a photoplate so if electron goes through it there will be a trace.
The electron acts as a wave so it has finite probability to pass through any of the holes if they are close enough. If it goes through the first hole it interacts with the first photoplate. This interaction changes its wavefunction so that now it has zero probability to be found in another hole and there will be no trace on the second plate.
The interaction (=observation) has already happened. Even if the photoplate will be processed in a year, or even will never be seen by a human, the electron do exist in the first position not second.
I suppose when you say "observe" here you mean "determine the position" since when we see object we see it in some certain place.
The Uncertainty principle says that coordinates of an atom can not be measured exactly but this does not mean the atom does not exist. The atoms manifest themselves in many interactions (see this discussion) and we can say that they do exist even though we don't know where exactly.
We can see things because atoms interact with the light, i.e. the light measure their positions. The accuracy of this measurement is limited to the wavelength but it is enough for macroscopic observations. In electron microscope one can see separate atoms (the uncertainty is less than the distance between them).
Just a little different way to think about observation of a quantum system:
In the quantum world, every process is reversible. As a result of that, information cannot be copied for you to observe. It can only be "rearranged".
So if you have object A (like a qubit) that can be in one of two states |0> and |1>, and you want to copy its state into another two-state object B, that operation cannot be reversed because, in so doing, B's prior state was lost.
So any reversible operation that moves A's information into B necessarily takes it away from A, in such a way as to remember B's prior state, thus disturbing A.