I went up on the roof and saw pieces of shingles torn off but
there were shingles below them (two layers).
How do I find where the roof leak is so I can patch it.
Are there telltale clues on the roof or do I have to guess?

You have to go into the attic. That's where you will see the leak. Then
you have to find a way to mark the spot (if a nail is coming down there
you might bang it back up, so on) so you know where to work on it from
above.