I am now learning my first vocabulary and I am a bit freaked out by the amount of different readings.
Not only because of onyomi and kunyomi but also because each of them has alternatives sometimes.
Like this one WaniKani / Kanji / 下
It has 6 different readings…
So it’s tough to keep track. How do you deal with that? Why so many alternatives?
Not to scare you too much, but that’s just the ones WK teaches. There are actually more…
It comes with experience. Every language has some weird things that are tough like that, and this is probably one of the toughest in Japanese.
It’s because of how kanji and the Japanese language came to be used together. Japanese had no written language until they borrowed kanji from Chinese.
Japanese people went to China many times over hundreds of years, so each time they studied kanji and returned, they encountered slightly different pronunciations of the kanji. This is natural, since languages change over time, or because they went to different parts of China, plus they had to make these Chinese pronunciations fit in the Japanese pronunciation scheme.
When they began to write their own native Japanese words with kanji, this also introduced multiple readings, because many different words can fall under the same general concept of a single kanji. “Down” is a very broad concept, so a lot of ideas fit within it, and therefore you get more readings.
WaniKani tells you for each kanji whether you should learn the on’yomi or the kun’yomi readings with it. In this case, it’s just the on’yomi readings. You’re only supposed to learn the kun’yomi readings here once they pop up with vocabulary words. Spacing them out like this makes it easier, I think, and the vocabulary words also come with mnemonics for the kun’yomi readings.
I’m actually not entirely sure whether or not you’re supposed to learn both on’yomi readings with this kanji, but I usually just learn one of them (the one for which there’s a mnemonic) and handle any alternatives (I haven’t seen a kanji where WaniKani provides more than two on’yomi readings) like I do with the kun’yomi readings, I learn them once they appear in vocabulary words.
With the vocabulary you will eventually learn all the readings(at least, most of it). I know it seem intimidating but don’t fret too much 
Yeah, just to reiterate what others have said and reassure OP, it comes with time. I was super overwhelmed at first, but even at my low level 6 it’s starting to get more natural for me. You get to know the patterns of which reading fits where and it gets to the point where in lessons you can actually guess which reading it will be sometimes. Just focus on the mnemonics and don’t worry about the rest until WK teaches you a new mnemonic with the vocab. Trust WK! 
It got a little lost in the answers above, but most kanji only have two readings, on’yomi and kun’yomi. (At least that’s all you will need to know here on WK.) There are some that have two or three different ones, but the majority are pretty easy to keep under control. 下 is a special case because 1) there are some many more readings than most other kanji on WK and 2) you’re still getting used to all of this so it seems really overwhelming.
Some other kanji that will completely frustrate you will be 日, 人, and pretty much all of the counters. Just keep at it and you’ll get through it. がんばる!
I agree with the others that it comes with time. As someone who has learned several languages non-natively, I see it a bit analogous to the English language. Each letter in English, for example, has multiple “readings”, or pronunciations. You actually never quite know how to pronounce something until you hear it at least once. For example, each “e” in “Mercedes” is pronounced differently. How would you know how to pronounce it without hearing it once? You wouldn’t.
At least with Japanese, the phonetic kana can come to the rescue so you don’t have to literally hear the word, just see it written in kana.
Over time, these things will become second nature - but you do need a lot of exposure.
And I’m an English native.
Though I’m a low level here, I’ve been dabbling in Japanese for a long time and know quite a bit vocabulary at this point. I’ve found that at first it really feels overwhelming, but you will also begin to notice some trends in the language too. Its important to remember that kanji =/= vocabulary. Kanji was attached to preexisting vocabulary and new words brought over from China, and it just so happens that some of those vocabulary words use just 1 kanji and no kana. That’s why kanji can have multiple meanings and sounds. You’ll notice after a while a trend in how those sounds are, but its not really something you can force effectively, you have to let it happen naturally.
That’s why its really important right now when you’re doing your mnemonic to really hone in the meaning of the vocabulary and the sound attached to that specific vocabulary through the story, and just simply use the kanji as a vague guide for meaning (or sound potential when grouped with other kanji).
Also its a good idea to look at the sentences too, and potentially look up more sentences. Once you know more grammar as well, you’ll notice a trend in its usage and get a better sense of a word such as transitive and intransitive verbs.
There are a lot of vocabulary words using 上 and 下 for instance, quite a bit more than shown on WK, but they make a lot more sense when you see how they’re being used for specific ideas when you see them in their sentences and how they’re used grammatically and remembering them as separate vocabulary words will be a lot easier then too.
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