Atmosphere and mood are highly subjective. For the purposes of this answer, we will define Atmosphere as sense of place and mood as sense of feeling. Additionally, Heart of Darkness is about 40,000 words long, so there are many, many examples throughout the text. One of each will be provided here, which should inspire deeper reading.
Atmosphere: For a sense of place, the prose should be simple and direct. There is a certain amount of license allowed for longer descriptions and metaphor; "purple prose" is often seen in longer novels, but Conrad's prose is short and very descriptive:
"I avoided a vast artificial hole somebody had been digging on the slope, the purpose of which I found it impossible to divine. It wasn't a quarry or a sandpit, anyhow. It was just a hole. It might have been connected with the philanthropic desire of giving the criminals something to do. I don't know. Then I nearly fell into a very narrow ravine, almost no more than a scar in the hillside. I discovered that a lot of imported drainage-pipes for the settlement had been tumbled in there. There wasn't one that was not broken. It was a wanton smash-up."
The jumbled pipes in a narrow ravine, the artificial hole with no purpose; each of these is simply described and solidly realized in the description. No extra words, no glorified metaphor, just a couple of holes that Marlow almost falls into. They serve no higher purpose in the story but they establish the terrain he is traveling and the activities that may have happened there. We don't need to know the composition of the dirt, or if the pipes are corrugated or smooth; the simple description is all we need to visualize the place completely.
Mood: For a sense of feeling, the license for metaphor is greater. Less significance is placed on description and more placed on the feel generated by the words. A feeling can be created using phrases that have little meaning in the larger text:
"The smell of mud, of primeval mud, by Jove! was in my nostrils, the high stillness of primeval forest was before my eyes; there were shiny patches on the black creek. The moon had spread over everything a thin layer of silver -- over the rank grass, over the mud, upon the wall of matted vegetation standing higher than the wall of a temple, over the great river I could see through a sombre gap glittering, glittering, as it flowed broadly by without a murmur. All this was great, expectant, mute, while the man jabbered about himself."
A jungle, thick and unfeeling, drenched with mold and moonlight, yet completely silent while the bricklayer talks. His words echo in the night, even reflecting off the silver moonlit mud, and fill the silence as easily and uselessly as crickets or night-birds. This is purely a sense of feeling, of words emptying in a cold impassive jungle, by a river that flows eternally without care. Is the mud important in the text? Will it be a key part of the climax? Does it matter when we have a sense of a bleak, entirely inhumane world which simply doesn't care about a bricklayer's life story?