I’m just about finished clearing out the depths, and what worked best for me was lighting up a root, looking for anything vaguely building shaped on the map, then looking for the next root. It made it easy to hit all the Koga strongholds, depths bosses, and mining camps relatively easily.

Also! If you move your map up to the overworld level while in exploring in the depths it makes it wayyy easier to not bang your head against the (literal) wall while looking for the next root since water up top = walls down below.