How could a layer of meaning found in Heart of Darkness be read and interpreted?

This is both a great question and a tough question to answer, as there's a lot going on in Joseph Conrad's Heart of Darkness and multiple different layers of meaning could be manifest at the same time. Some of the major themes that many scholars choose to focus on in Heart of Darkness include: race, the "civilized" world vs. the "primitive" world, alienation/isolation, and colonialism. In truth, the best way to uncover threads of these themes and the meaning behind them is to remind yourself that you're going to encounter them at some point, and then to read carefully and closely. If you mentally prepare yourself to encounter these themes, you're going to be better at looking for and finding them. 

As an example, let's examine the theme of colonialism. The following quote is a good place to start:

They were dying slowly-it was very clear. They were not enemies, they were not criminals, they were nothing earthly now, nothing but black shadows of disease and starvation... Brought from all the recesses of the coast in all the legality of time contracts, lost in uncongenial surroundings, fed on unfamiliar food, they sickened, became inefficient, and were then allowed to crawl away and rest. (38)

In context, we find that the "they" in this passage refers to native peoples who had been subjugated by the invading colonizers. As such, in this passage, we can infer that Conrad is making a statement about the theme of colonialism and the meaning behind it, which, in this instance, is really rather wretched. Despite the apparent "legality" behind the colonial forces' work, it's apparent that their rule is characterized by the cruel subjugation of native peoples. Indeed, Conrad seems to be questioning the idea that anything so cruel could be legal at all: how could enslaving, starving, and effectively killing a human being be condoned by law? As such, we see that, by closely reading the passage, we're able to uncover a thread of meaning: for Conrad, colonialism is an evil enterprise that uses a corrupt definition of law to justify its cruelty.

Try thinking about some of these themes (colonialism, race, etc) while closely reading the book; unravelling meaning is tough, but the more you practice, the better you'll find yourself becoming!