So I am only level two but I just learned 一日. It doesn’t appear to have On and Kun readings but two different readings that Wanikani accepts いちにち and ついたち。I barely understand On and Kun as it is, but how would you know, especially without furigana potentially when to use one or the other? Yes I’ve read the Tofugu article on On and Kun and I still can’t keep them straight!
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This read might help you:
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On and Kun readings apply to individual kanji. 一日 is a word. In fact, it’s two words that happen to be written the same way: いちにち “one day” and ついたち “first day of the month”. You distinguish these the same way you deal with “different words both written the same way” in English: from context. In “A dog’s lead” and “a lead weight” nobody confuses one word with the other, and it’s the same thing here.
For On and Kun readings more generally: my suggestion is to not worry too much about them. Concentrate on learning the vocabulary; as you build up vocab the patterns will become more obvious and will help to make the learning a bit easier. (But they’re only ever patterns that make it easier to make correct guesses; they’re not iron rules you can rely on. In the end you just have to learn vocabulary…)
One final note: the early levels have a lot of weird special cases and kanji with lots of readings. This is because the early kanji are the very common kanji, and the very common kanji are the ones with the most special cases and exceptions. After a while it settles down a bit.
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As far as I know, 一日 is the only one that changes readings when used to represent a number of days. The other day numbers retain 訓読み when counting days if they used it when representing a day of the month.
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I had no idea one meant the first day of the month instead of “one day”. I thought they both had the same meaning from the way it was presented. Thank you for your answer, it helps a lot! (So did the others 
)
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There isn’t a guaranteed way to do this but I do have some strategy for guessing which reading it is.
Words containing exposed hiragana, including almost all ichidan/godan verbs, tend to use kun’yomi. (生む)
Words containing only one kanji tend to use kun’yomi. (人）
Two-kanji compounds are somewhat divided.（人生, 交代、出口、水着) These are the trickiest to determine, but I try on’yomi first. Don’t quote me on this, but I think する verbs use on’yomi most of the time.
Words that consist only of several (3 or more) kanji tend to be on’yomi. For instance, anatomical words such as 上腕二頭筋 (じょうわんにとうきん, biceps).
In terms of telling the readings apart, my definitely-not-foolproof way of guessing this is that on’yomi can often be represented as one English syllable (きょう、とう、きゅう、しゅう、かん), but kun’yomi often cannot unless they are one kana (くら、は、どろ、みず）. You can also look at the Jisho website or WaniKani’s page about the kanji.
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I literally just realize this and I’m on level 9!! I wish I had learned it sooner, because I think I would have learned vocab faster. So far,most vocab with two kanji and no hiragana- are usually onyomi. And onyomi is usually what we are taught first. If there’s a hiragana character after a kanji, it is more often kunyomi. I really think this concept should be shouted from the mountaintops. I never bothered to learn which was onyomi and which was kunyomi and I really should have been paying attention earlier!