An embedded question is a question that is indirect because of some other feature in the sentence:
I'd like to know where her office is. (Here, 'I'd like to know' embeds the direct question 'where is her office' and it becomes indirect.)
A cleft sentence is where a sentence is broken up into two clauses:
Mike did it.
It was Mike who did it.
The second is the cleft sentence, where the original single clause sentence has been broken into two.