First of all, when you have an assignment for writing a research paper, be sure you know the requirement for what type of paper is required. Is it an argumentative/persuasive paper, an informative paper, or a problem/solution paper? If the type of paper isn't specified, then you should decide on which type you will write.
Next, you will need to develop a thesis statement. This statement provides the overall direction of your essay. For an argumentative paper, your thesis statement needs to take a stand on a controversial aspect of the topic, using evaluative words such as "should," "better," or "more." For this topic, your thesis could be "Prayer should be allowed in public schools" or "Prayer should not be allowed in public schools." For an informative paper, you don't need to take a side; you can simply lay out the controversy. Your thesis statement could be something like "Prayer in public schools is a controversial issue with vocal proponents and opponents." For a problem/solution paper, you would seek to find a solution for a problem related to the topic; an example would be, "Although many people feel prayer in public schools violates the First Amendment, there are ways students can pray without causing legal problems for their school."
Once you have your thesis statement, develop a sentence of division or map. This will express the basic outline of your paper, naming its main topics in a single sentence. Find two to four supporting points for your argument or explanation or solution. Exploring websites such as procon.org or debate.org can help you explore the issue and decide on topics that support your thesis. For example, if you were arguing for prayer in public schools, your thesis statement/sentence of division might read: "Prayer should be allowed in public schools because it does not violate the First Amendment, students who don't want to pray can opt out, and students who want to pray have the right to free exercise of religion and free speech." Write a sentence of division to expand upon whatever thesis statement you choose.
Now you have the basic structure of your paper. If your paper needs to be four pages long, you would compose a page for each of your three supporting arguments (if you have three). Your introduction would be a half-page and your conclusion would be a half-page, giving you a total of four pages. Adjust the length of the sections accordingly to meet the length requirement of your assignment. For each of your supporting points, do research to find sources that agree with your point. You may also find sources that disagree with you and refute them. Use summaries, paraphrases, and direct quotes from those sources to develop your argument. Use the documentation style, such as MLA, that your class requires. Add a Works Cited page at the end.
Purdue OWL has excellent resources that can help you in your process.