I think nobody would use full names while talking to each other. At the most last names or just first names. I would appreciate it if the author took this into account.
Lol this story's comments are sieged by 13 year old kids, not to mention two of them are here just because they hate the author. The naming sense isn't good but honestly, I haven't seen a single book with good naming sense. Example: Harry Potter, Percy Jackson, Annabeth Chase are all horrible names but they have meaning in the story (well Harry Potter didn't, they just had to find the most normal names ever which is part of why I dislike the books as they're cliche wizard crap)
I'm not perfect at commas either, so take the grammar mistakes I point out below with a grain of salt.
1. All of the students there, deserved to be disciplined. probably shouldn't have a comma. It's awkward.
2. Just getting an earful, was only, one of the minor problems that could have come his way. I don't think this sentence needs any commas. Try reading it aloud while pausing briefly during commas. It sounds awkward with them in this sentence.
3. It wasn't by any means, natural to keep calm after seeing a fellow student they grew up with, die. Another sentence that sounds awkward with commas.
4. In the past when he had gone on his first day of middle school, an earthquake had hit the school, sinking most of the building underground and leaving him, safe and sound because he was late. No comma needed before the word safe.
5. It was completely different from the smothering feeling inside the school as if what they were breathing, was dirt and dust instead of oxygen. Remove the comma before was. Add a comma before as if.
6. No wonder the fatso die. should be died.
7. His current voice was, even more, colder than his usual voice. Remove both commas and the word more. The word more is redundant in this sentence.
8. If the students, were to place a name on the green stuff, it would appear to be, colossal grass. Remove the comma after students and before colossal grass.
9. Standing in disbelief at the sight that greeted them,. Not 100% sure but think you meant to say staring not standing?
10. the dirt craved in as a bug twice the size... Think you meant caved, not craved.
I don't have time to review your other chapters. Gotta catch some sleep got class soon. When it comes to commas and you're unsure, just read the sentence aloud. Anywhere you pause will typically have a comma. If you're still not sure, I personally believe less is better. There were some other questionable sentences for commas I didn't list. This was because I was either unsure, thought they were debatable, or thought they worked well with or without it.
Your novel is interesting. Good luck and keep on writing.
Lorist_Norton