Bill R:

What the court has held as far as having a "prayer meeting" is that religious groups have to be given the same access as any other group to school property. So if the chess club has a meeting during school hours, a prayer group would have the same right. But, of course, groups like that are extra-curricular, so they aren't going to be meeting during school hours.

The same goes for school property after school hours, though.

Students or anyone else on school property has the right to read a Bible or say a prayer before eating. And they have the right to say it aloud. What they don't have the right to do is disrupt the education of any other students.
That's the principle behind court rulings on religion in school. Not worship.

So if a group of students stood up in the cafeteria and started saying a prayer before they ate, the teachers or staff in the cafeteria would have to decide on the spot whether they were disrupting other students.
Since anyone could sit and parse a question like that until the cows come home, they are almost always going to stop the potentially disruptive activity because by law they can't let one student disrupt another's education.

It puts a big burden on teachers and administrators. A student is allowed, for example, to talk about their religious beliefs with another student until it becomes some sort of religious harassment. Where do you draw the line?
So some make mistakes that get blown into misconceptions about what is and isn't allowed, and the questions keep circulating through the courts.

The Supreme Court has held that a religion doesn't require belief in a Supreme Being. So secular humanism is considered a religion. But, for example, Buddhism and many Native American beliefs also don't hold with the idea of a Supreme Being in the Judeo-Christian sense.

I don't know what you mean by the practice of atheism in the schools, but students aren't allowed to harass anyone over religious beliefs even if they're atheists. No school administrator would be allowed to stand up at a graduation and lead everyone in reciting a rejection of religion.

If on the other hand you think of practicing atheism as the absence of practicing a faith -- not praying is practicing atheism -- well that's a philosophical discussion. But not praying is not going to disrupt any other student's education.