Note that the word order emphasises "в школі" bit. The neutral sentence would be "мій брат зараз у школі".
So the в/у change isn't used too much? Or I guess I'd like to put it as - it's not used as a strict rule?
"в школі" is actually a very bad thing to say. Three consonants! How one should pronounce that :)
But this course is quite inconsistent with a lot of things