Explaining why some atoms combine and others don't is practically the entire basis of chemistry. As you can imagine, there is no catch-all, simple explanation. You'd have to start from square one with a general chemistry text and just start reading.
Based on your description, I would suggest investing in a basic organic chemistry modeling kit. Most of the atoms in the upper right quadrant of the periodic table WILL bond together in various ways (Except the far right column.) and they are represented in most modeling kits. You can then look up some basic molecules that maybe you've heard of and see if you can build them with a modeling kit (acetone, ethanol, octane, chloroform etc.). I think this would be an appropriate place for a 5th grader to start tinkering around. You're not going to learn the nuances of orbitals and chemical bonding this way, but you will start to learn things about the types of things that are generally allowed (how many atoms a carbon will bond to, what a double bond is, etc.).
Search amazon or ebay.