An atom cannot be seen with a microscope, using ordinary light. Grains of light, also called photons, are simply too big to give an image of atoms. As it is difficult to understand for beginners, I could use a simple image.
Imagine you are living in a cavern like our ancestors, the prehistoric men. To draw a hand on the wall of the cavern, they filled their mouth with wet charcoal powder, and they spit this black mixture on the hand against the wall. They obtain a black-and-white image of the hand. If they had used pingpong balls or basket balls, instead of charcoal powder, they would never have obtained an image. These balls are simply too big to pass between the fingers.
It is exactly the same for us. Photons from usual light are too big to allow us take an image of the atoms. Much smaller photons are needed. For example, photons from the X-rays are small enough to allow a photographe of the atoms, But these X-rays are not part of the usual spectrum violet-blue-green-yellow-orange-red. So, unfortunately we will never develop a microscope which could show us atoms with ordinary light.
Now, to go back to your question, the first scientist to give a description of the electron in an atom is Niels Bohr. He proposed that electrons are turning around the nucleus like the planets around the Sun. He made calculations about the mass, the charge, the speed of the electron turning around the Hydrogen nucleus, and the distance electron-nucleus. These calculations give good results with the Hydrogen atom when compared to energies and distances as measured by X-ray or similar techniques.
So this theory was soon extended to other atoms giving electrons rotating on circular orbits as you know. But the calculations made with other atoms gave results that are not so good. Qualitatively they are good enough to make drawings like the page you mentioned, where electrons are like planets. It allows to show nice description of molecules, using Lewis method. You probably know these drawings, with dots and bonds.
Today we think that electrons are not turning. They "exist" on sorts of clouds, called orbitals, centered around the nucleus, and whose average center of mass is near the nucleus for the first electron, so that the elctrons are more and more repelled away from the nucleus, when an atom has a lot of electrons. Alas, this description is not easy to visualize. That is why high school chemistry is still often taught with the old Niels Bohr theory, although it is not perfect. Showing the shape of these orbitals in 3 D is not easy to do at a high school level.