For formal English, the second is correct. Your class book probably has a section called indirect questions. Direct question: What is the main idea of this article? Indirect question: Can you tell me what the main idea of this article is? If you have a copy of the well-known book English Grammar in Use by Murphy, consult unit 50.

Written, the first is a common word-order error of non-English speakers. In speech you could say something like: Can you tell me? (hesitation) What is the main idea of this article? where you are essentially asking two questions and abbreviating the first: ‘Can you tell me the answer to the following question?’

Both are correct. There is no difference in meaning. The only difference is a rhetorical one. The first sentence states the question directly: "WHAT is the main idea?" The second sentence states it indirectly. The first sentence sounds more emphatic. When you read the first sentence, you naturally place a strong emphasis on the word "what", but you do not do that when you read the second sentence.