I’m not having any troubles remembering the pronunciations for each Kanji, just which one’s which. Is there any method to remember which pronounciation is which? I also don’t know which situations are right to use either Kun’yomi or On’yomi, I’ve heard something about when it’s mixed with hiragana it’s one or the other but I don’t know…
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Stick with it. It will become pretty evident eventually.
The background shows what it’s looking for:
Pink - Kanji and On’yomi
Purple - Vocab and Kun’yomi
Normally the Kanji and multiple Kanji words will use on’yomi, but there are enough exceptions that you need to be aware of it, especially with body parts. Words with kana will usually be kun’yomi.
I think Level 5 was about the point that I started having less of a problem keeping them straight.
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Normally if two or more Kanjis are together the Onyomi is used. If there are hiragana attached it´s kunyomi.
But there are tons of exceptions. E.g. Kanji for bodyparts useally the kunyomi is used,but not always. Sometimes in a word kunyomi is used for one kanji and the other is onyomi.
Also there are readings that have nothing to do with kun- or onyomi like 今日(kyou) or 昨日 (kinou)
I´m remebering the readings with vocablurary instead of the kanji alone.
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Check out the post that describes the history of the two and some of the patterns that they follow, this helped me a lot. I am still having trouble myself identifying the patterns, but like people mentioned this only comes with practice.
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Generally, when kanji appear on their own they use kun’yomi. When they appear in a compound word, they usually use on’yomi. When a word has hiragana in the middle of it, it usually means the kanji takes the kun’yomi reading.
For example, 安売り (やすうり) - “to sell cheaply”. The individual readings for these words are the kun’yomi readings, 安い (やすい) meaning cheap, and 売る (うる) meaning to sell. The okurigana at the end tells you they’re going to use the kun’yomi readings and not the on’yomi readings. The on’yomi readings for these kanji are アン and バイ respectively.
When you learn more vocabulary words you’ll start to notice the patterns pretty quickly, and guessing which ones take which readings becomes one of the most fun parts of WK in my opinion. Vocabulary are the cherry on the cake of kanji that is WK. Hope this helps. 
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I try to use vocabulary with weird pronunciations a lot to remember the reading.
Words such as 先ず (Mazu) or 先 (Saki) because the (Sen) reading is so ingrained in my brain already I read all as that.
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The way I remember. Kun’yomi is the “Japanese” reading. It’ll usually be the reading when the Chinese character has hiragana with it. I remember its the Japanese reading because - kun is added at the end of names in Japanese when speaking about boys.
On’yomi is the Chinese reading. The pink “kanji” questions ask for the Chinese reading. Usually a word will be read with its “Chinese” reading if it’s just kanji characters - no hiragana.
I hope this helps. When I first started I was pretty confused. I stopped wanikani for nearly a year and just started back again last week I reset my profile one level down to just get the hang of it again and that’s when the stuff clicked (hopefully) though I still get some stuff wrong.
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Those readings are technically kun readings, words of Japanese origin that are applied to kanji characters, you just can’t assign any individual portion of them to any individual character, because they are kun readings that only take effect across that pair (or more) of kanji. The term for these is jukujikun (compound kun).
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thanks for the info 
I didn´t now this before
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