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Wouldn’t call them “most common”, it’s more the reading the wk team considered the most appropriate to teach. Either because it’s actually just the most common reading of the word, or because 9 times out of 10 the words you’ll be learning that use it will be using that reading.

Wouldn’t worry about mixing them up yet honestly. As you learn more and more words and you get more and more patterns into your brain, you’ll be able to recognize 1) which type of reading you even need there likely, onyomi, kunyomi, whatever 2) what type of reading you’ve even learned with the word and 3) based on the shape, what’s the likely onyomi reading of the word. This last point is called “Semantic-Phonetic composition”, there’s a userscript for it if you care (here), though it’s not at all strictly necessary.

One thing I did when I was a bit earlier in WK was trying to guess what the reading of a word was going to be before getting to that tab. It helps reinforce the pathways in your brain related to that kanji reading and the pattern recognition for the readings in general.