So I think this helps me like 90% of the times! And I want to know if there is any reason for this or even if it a good trick.
So when the kanji has the same reading for on’yomi and for kun’yomi, when you use that kanji with another one forming a jukugo, we use the kun’yomi reading for the two of them.
My mind can’t process this right now.
Care to give some examples? 
Huh? This doesn’t really make sense. Are you possibly confusing the vocabulary readings as always being a kun reading? Because that’s not true.
Im going to give examples:
That’s not correct. The onyomi of 糸 is シ and 朝 is チョウ. You seem to have mistakenly conflated the kanji reading WK teaches as always being the onyomi which is not correct.
Oh yeah, sorry, you are completely right! I don’t know why but I thought that when you learned the kanji you would always learn the on’yomi way! My mistake xD
Yeah, WK teaches what they consider to be the most common reading. That will often be onyomi but not always.
“WaniKani almost always teaches the on’yomi reading with the kanji. Then you’ll learn kun’yomi readings later, with vocabulary words.”
From the WK FAQs pages: On’yomi and Kun’yomi Readings | WaniKani Knowledge
A small number of kanji do have the same onyomi and kunyomi, but it’s fairly rare. Some examples with minimal research:
死 - both readings are し - 死ぬ / 死亡
差 - both readings are さ - 差す / 差別
架 - both readings are か - 架かる / 担架
On the lesson page, under the reading tab, it will say whether you are learning the on’yomi or kun’yomi above the hiragana reading
The split between on’yomi/kun’yomi on Wanikani’s kanji reviews is something like ~1700 on’yomi, ~300 kun’yomi. The idea is that you hopefully learn whichever reading is more useful to know when you see the kanji in an unfamiliar word.
I’d recommend using [Userscript] WaniKani Katakana Madness, because with it, you’ll passively learn whether each kanji reading is on/kun based on whether your answer appears as ひらがな or カタカナ. You’ll also get more exposure to katakana, making it easier to read at a glance 
Uh thats nice! Thanks a lot! Can you just tell me the steps to install it?
Just download a script manager for your browser (I use Tampermonkey for Chrome), then download the userscript from the link on the page in my previous comment.
I’ll give my thanks as well. I must’ve missed this script when I browsed the script list previously.
Still, with any previous kanji knowledge, it is fairly frustrating to go through lessons and reviews by trying to first input on’yomi and have the system ask you to try again 
. (There should be a more clear visual clue as to what is asked…)
On this level 8 alone, there are five kanji that teach the kun-yomi and many times I doubt the WK reasoning of choosing the kun’yomi. I kinda get 雲, as it is a standalone word. But for kanjis tied to verbs like 買, I can’t see a logic to learn is as か , since you’ll never see it as a standalone か and 買う kan be taught as vocab soon enough… Also the reading ばい is not rare at all… (sorry, this turned to a rant)
Actually, I wish there was a setting like “No, I do not want the recommended path. Teach me always on’yomi first, if it exists” 
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