I understand they used dark energy to show that the universe is expanding and all. They also say if you remove all the atoms etc out of a contained body of space it wouldn't be empty because dark energy would still be present. But how do they know and what is it?

Dark energy and matter is a hypothesis to make certain equations solvent. They were hypothesized to exist after it was found out that the universe doesn't have enough mass to be the way it is. The amount of mass that was missing and we couldn't observe, is what was called dark mass. Dark energy is of course then coincidentally there, as mass essentially is trapped energy and energy is released mass (E = MC2).

It is not known what dark matter or dark energy is, as we really have no way of observing it. How it acts can be indirectly observed, but it is still a very obscure chapter in the physics world.

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You know the spirals in our galaxy? The area between those spirals is filled with "dark matter", as of now there is no way to test it... but just a few years ago we said the same thing about anti matter

We discovered anti-matter in what, 1932? And Dirac proposed their existence as a direct result of the fact that there were inexplicable solutions to the Dirac equation in 1928. Both Dirac and Anderson (the guy that experimentally discovered the anti-matter) separately received Nobel prizes in Physics.

I don't know that it's correct to say that the area between spirals is "filled with dark matter" either. We have the spirals that we do because of the conservation of angular momentum. As gravity started drawing matter together after the big bang, it started spinning because of the fact that there wasn't a spherically symmetric mass distribution, so the center of mass was not at the physical center of the areas of gas that separated into the separate galaxies.