Is English your first language? Your writing is a little stilted and difficult to understand. There are a number of tutorials on the website. If Pokemon Essentials is broken then I recommend hack tools or the disassembly. Tileset numbers are just numbers to distinguish different tilesets from one another, they're nothing special. What exactly are you trying to do? Just make a map look slightly different with a couple scripts? It sounds like he already knows how to alter tiles and wild pokemon, you can do a fair bit with that.
How do computers work? Oof. That's a big question that honestly isn't very relevant for hacking since nobody programs in binary these days. Or, wait, you mean the computers inside the game? The easiest way to hack is to just open up existing maps and look and see how they do it, and remember that there aren't just events visibly on the map, but also 'on load' header scripts. However I vaguely remember you can manually add PC 'visible' script events too; it's been a long time tho'. If you start with an existing base, then you don't need to add any PCs, there will be plenty of pokemon centers and there's honestly no good reason to mess with a pokemon center for a first hack as existing ones work fine.
I started coding without any help from my parents when I was just a couple years older than him. Encourage him to study hard so he can do things like understand tutorials by himself, and let him know it may take years before he's good enough to do everything other hackers can do, so the best thing to do is to be inquisitive and patient at trying different things and seeing what does and doesn't work, and in carefully searching through tutorials for information. Tell him that for a first hack he may need to settle with altering pokemon, text, minor map edits and trainer parties, a lot of people do, but if he gets good at coding, then he can use the disassembly and change almost anything about the game.