Atom Theory vs Quantum Physics This never really occurred to me until now, so maybe it does not categorize as a really important question, but, according to Quantum Mechanics, anything that is not observed exists as a probability until observed. 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 you're looking at something with mass, so does that mean (supposedly) that atoms are only probability until you can observe them with the proper equipment, even though on a smaller scale thats what the things you are observing are made up of?
 A: "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 very accurate analysis of materials possible. I think you should read this but you can also find very beautiful images on the internet.
A: Observation
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.
Uncertainty

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

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).
A: As this came up again due to a troll whose contribution was deleted, I would like to clear up a basic misconception in the question.

according to Quantum theory anything that "is not observed is probability until it is observed when it condenses down into matter".

The misconception is on what probability means:

Probability is a measure or estimation of how likely it is that something will happen or that a statement is true

At this actuarial life table the probability of death within one year is given in the first column, by age. Take a 30 year old male: he has a probability of dying within the next year of 0.001419 . Does this mean that this person does not exist until he dies? 
The probability of finding an electron in a specific (x,y,z,t) is given by the square of the wavefunction. This does not mean that the electron does not exist . It means that this is the extent of our knowledge about its existence until we probe it with an interaction. When the electron is tied to an atom the probability defines the orbitals, i.e. the allowed locations where the electrons can be.  
The quantum mechanical entity that is the electron always has a mass and quantum numbers. Observation brings out the particle aspect of it or the wave aspect of it depending on the experiment.
A: 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.
