I love teaching about molecules and atoms, kids seem to love it too! Talk about how everything is matter; they, their books, desks, clothes, the air, etc. and matter is made of atoms. Here is a GREAT website that has a ton of information and games, written at a level the kids can understand: http://education.jlab.org/
After they have an idea of what atoms are, we construct some using pipe cleaners (electron shells), pom-poms (different colors for protons and neutrons) and beads (electrons). The kids love putting them together and they look great hanging from the ceiling.
I demo an atom by putting clay globs on the board .... I use two colors, one for the protons and one for the neutrons. First I start with something like Helium [only 2 protons, neutrons, and 2 electrons. I put two red globs of clay on the board for the 2 protons, then I put two green globs of clay on the board for the 2 neutrons. And now for the "great part" ..... the visual. I take a clear glass bowl and put two smaller blue globs of clay on the inside of the bowl and place it over the red and green globs on the board ..... TaDa ..... an atom! I start with Helium because it only has 2 of each. Don't start with Hydrogen, because it doesn't have a neutron. Then I expand this to do Carbon . Do the demo. the same way, putting 6 red globs and 6 green globs on the board. When it comes to the electrons, put 2 on the inside of the bowl and then put the other 4 on the outside of the bowl. In this way you can introduce energy level and show that only 2 go on the first level. Don't worry about the next levels because there will always be some student who will wonder how many electrons fit in the second level. Then you have your nice segway into energy levels and the amount of electrons they hold. In the end, we draw atoms and I assign them one to draw for homework. My fifth graders really like this.
This website has some ideas on a great way to teach about atoms and molecules. It's called Matterville. It contains a story about a city and its inhabitants. I used embroidery hoops and printed out some clip art to represent Perky Patty Proton, Nerdy Nelda Neutron, and Enraged Elliot Electron.
I just love chemistry. While we can't see the atoms and molecules themselves, we can see their behavior and that's so fun.
One book I like is Anita Brandolini's Fizz, Bubble, and Flash which discusses chemistry. Our public library has it and it's published by Williamson.
Molecular action is as easy to see as dropping some food color in a jar of water. Without stirring, the molecules' motion mixes the dye throughout the jar (cold water is slower in doing this than hot water).
Another fun thing is to give students a pie tin with milk (skim will work, but milk with fat does better). Drop a few drops of food coloring in the milk and the dye just sits there. Dip a toothpick into some liquid dish soap and then put the toothpick in the dye drop in the milk and the dye drop dances around quickly, a sort of fireworks in a pan. THat's because detergent molecules hang onto fat (milk) on one end and water (the dye is mainly water) on the other end, separating them. THat's molecules in action.
You can always dig up a few polymer (long chains of molecules) projects as you go along. Polymers are really cool. Plastics are polymers as is wood. Try ripping a plastic shopping bag like you get at the grocery store. Pull in one direction and it simply stretches (you're trying to break those long chains and they sure are strong) and pull another way and it easily rips (you're attacking the weaker bonds between the chains).