The physicists still need to understand the area around the nucleus, but they are usually concerned with the forces at work keeping that nucleus together. Once they understand those forces, they often try and create new types of fusion and fission reactions. This is the energy released when the nuclei of atoms split or are fused. As you know, the nucleus is made up of protons and neutrons. Huge amounts of energy are released when either of these reactions happen.
Fusion reaction create much of the energy given off by the sun.
The Uranium comes to the reactor in small pellets, those pellets then go into fuel rods. After the reaction, the leftover material is very radioactive. Scientists cool the Uranium and Plutonium for one year in a big pool of water. After enough time has gone by, and the radioactive materials have cooled down, officials have to bury the nuclear waste very far underground. They bury them so that the radioactivity will not contaminate the surrounding water or land.