How would atomists explain the difference between, say, chalk and cheese? How do they explain coming into being and passing away again?

Atomists would explain that chalk and cheese differ because they are made up of different atoms. This is because a certain kind of atoms for our sake we will call them atoms K mix bound together to form chalk and Atoms H form together to form cheese. They do not differ by our sense perception but by the atoms they are made up of. The atoms also differ from other objects by how tight they are bound. Soft bodied atoms are more flexible because there is more void in them.

They explain coming into being and passing away by using the same idea of atoms. When atoms come together and bound to each other they form a being and the being is therefore created. When atoms disperse and start to separate they are again passing away.