behind this?"
can we use this "what the reason behind this is?"
neither is correct. you may say, "do you know what the reason is for their leaving?" or,"do you know the reason for their leaving?" or, "do you know why they're leaving?"
2) can we use this "what the reason behind this is?"
no. but there are other ways of asking, such as, "what is the reason for this?" or, "what is the reasoning behind this?"
i believe you are asking about word order in direct and indirect questions.
direct question: "what is the reason behind this?"
indirect question: "do you know what the reason behind this is?"
there is one word order for the direct form 