Right after you climb down the stairs, the recess to the right (after you destroy the pots with flammable liquid).
From the Archive chamber, walk through the narrow passage between rocks, towards the location entrance. The document is in the corner, on the right.
In the chamber, in which you found the atlas, you can use the rope to jump over twice, from the rubble on the right side of the chamber, to the other side. Grab the pipes under the ceiling.
To get to the balcony above, you need to go to the chamber next to the main one, near camp Greek Fire storage. There, locate the climbing wall to a small balcony. Go left and follow the corridor to the document.
It is on the balcony above, where you have pushed the second container, with Greek fire, into the water.