"How can I make indirect questions?" - This is a direct question.
"Do you know how I can make indirect questions?" - This is an indirect question. Notice that the word reversal is always early in the sentence. Because "how" is in the middle, then we use a regular word-order.
"I want to know how I can make indirect questions." - It's not a question, so it follows regular word-order. However, we can still see that you are asking something, so it counts as an indirect question.