A good diagram of how a nuclear reactor works. The image links to the site, with more description.
This doesn't look very pretty, but it's a good demo of how a chain reaction can happen. They haven't shown the electrons in the material, just the nucleus of each atom:
This is quite a good video that shows one of the ways scientists can "see" atoms, by using a beam of electrons to scan them (remember: atoms are so small light can't bounce off them, so we can't see them using normal microscopes). The English in the video isn't perfect, but you should get the idea.
There are other ways of doing this, like where the electrons 'bounce' off the thing you're imaging, instead of going through. Here's an example of what you can see from these sorts of things. The first is some pollen, the second is an insect's eye.