Usually, 'had had' is used in causative form.
Causative form is used when we do not do something ourselves, but we arrange someone else to do it for us.
Let me explain it on an example:
We can say "he has fixed the car", what means that he did it by himself. While using causative, it could sound like "he has had the car fixed" what means that his car has been fixed but he wasn't the one who actually mended it.
When it comes to earlier mentioned "had had", the principle is the same but this time we have got past perfect:
"He had organised the meeting before I came" what means that he organised this meeting by himself, but if you want to say that someone organised it for him you can use causative form and it may sound like "He had had the meeting organised before I came."
I hope that my explanation exhausted this particular subject.