I've found the key to the safe box after I listened at the door. But now
I can't find the safe box itself. Where is it?
It's not there. Your mission is to make a copy of the key and leave with it,
so stick to that... you will the box later in the game.
How do I make a wax impression of the Key?
Behind the work shop in the cellar, there is another room (on the right) where you find appropriate material and tools for this task.
Where do I return the Safe Box Key to?
To the very place you picked it up from.
Where do I put the key back down?
Depends. There are five possible places; it varies from game to game.
You need to pay attention to Garretts commentary during the game;
the places are chosen randomly upon mission start.
Worst case you need to load your saved game or start the mission over.