Don’t think about it too hard.
No language has clear defined logical rules. English doesn’t. Japanese doesn’t.
However, there’s a part of your brain that’s wired to understand/acquire new languages.
Eventually, you’ll just know when 大 means おお、たい、or だい.
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I guess to piggy back on the original question, why do kanji have different sayings if they’re only building blocks? If it’s only a building block why have a saying (on’yomi) at all?
For instance. 大 kanji for big is said (たい, だい) but the kanji in this adjective for big 大きい is said (おお). Why not just たいきさ?
EDIT: p.s. this is my first post ever 
Why does ‘live’ have two different readings/meanings even though it’s spelled the same?
Why do the same letter combinations sometimes make different sounds?
Why do we even have silent letters in English? Queue is just the letter Q followed by 4 silent letters!
Languages have complicated histories.
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Because おおきさ and おおきい were existing native Japanese words for which the 大 was assigned and given that おお kun-yomi reading.
This may be a good article for you to read:
Japanese as a spoken language existed prior to the usage of Chinese hanzi as a writing system. That’s why you have the duality of readings.
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Thanks. Yea I read that article. I guess I’m digging to deep!
Thanks for the responses
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It can be confusing, but that seems to be what happens when you bolt on a foreign writing system to an existing spoken language. 
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I think of the kanji like the building blocks. I am not as skilled at Japanese as my boyfriend who has been studying for a while. However I can occasionally breakdown larger words, because I know the kanji associated in them. This helps me, figure out words I would normally now. So I think there’s a real benefit and seeing how things are structured as well as knowing the vocabulary.
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