Here it goes. You get to the first part of the school. It contains four secret rooms with extra content. You can see all the extra content in Extra menu. Basically, a secret room is a door that can be opened (Keep in mind that every door except for secret ones can't be opened). On mini-map you can see where exactly those rooms are. Also, I used to make those screenshots before 1.4 release, so you can't see zoomed version of this. Sorry about that.
First secret is in the big yellow doors that seem to lead us in the wall. You should probably open it. Advice: Try opening all BIG yellow doors you see.
Little storage room is the next secret. It actually has nothing in it but extra content.
Next secret is really close to the first one. I think you can easily see it so no advice here.
On one of the nasty corners you can find a door that leads to the toilet. Not too hard to notice.
After you've collected half of the shards you progress to abandoned part of the school. And it only gets harder. Here, you have only one secret room with extra content and other one as an easter egg (Though, I still recommend you to check it 'cuz I never really noticed if you get and S rank after opening that secret).
This secret is another toilet in another nasty corner. You know what to do here.
The room behind a wall with Agatha's face on board. You need to click on it in order to opem. How I said, this might be an easter egg. Still, just open it, it's not that hard, is it?
I decided to make a bonus. Here, I will show you how to get all achievements for Chapter 2!
Ahead of the Class
Here you just need to beat Elementary Evil level.
Peer into Darkness
You need to find one of secrets in the school.
When you're in the playground (Place, where Ring Altar is) and go behind a slide. Then, you should click on it you you will get the achievemnt.
This one is a toughie. You need to NOT touch the "Fake" portals when you run from Malak. 'Cause when u touch 'em, Agatha spawns and runs to catch you. You need to find a way where there is no portals and the you will get the achievement.
Too Cool for School
This one is simple. Just get an S rank on her and you're done.