how do atoms actually work?

There's the nuclear force, which gives the particles in the nucleus a strong attraction for each other.

Once you've got the positive nucleus, the negative electrons will be attracted to it.

but the electrons repel one another, which is why the atom takes up all the space that it does.

Put simply, the electrons are attracted to the nuclei.

and the nuclei are atracted to the electrons.

So neither is going to move far from the other, so atoms stay together.

Of course, in gases, the particles have enough energy to fly apart, and not enough attraction to stick together, but in solids and liquids, it's down to electrostatic forces in one way or another.

every matter is made out of atoms, you are, your computer, your pencil. you are right, they are very small. but they are great in numbers. you are made of trillions and billions of atoms.