“The Past Perfect expresses the idea that something occurred before another action in the past. It can also show that something happened before a specific time in the past.”

for instance, with your 2 sentences, the first one u wouldn’t have to use the word “had” since it doesn’t refer to any past action or a specific time in the past. so the answer would be, Father asked Timmy where he hid the report book.

for the second one, u would use the word “had” because it refers to a specfic time in the past which is “yesterday.”

ex. I had finished the novel before she called me.

finishing the novel happened in the past, before a specific event, “before she called me”

hope this helps. n my source is a great one too.