TL;DR The very broad answer is if it has two kanji it uses on’yomi readings. If it’s one kanji by itself or with some extra kana on the end it uses kun’yomi.
If it has multiple readings like 出る/出す you really just have to remember the difference. I’m sure many people will come in with more advanced technical answers for you. Good luck!
You’ll just learn. It’s like the knowing the difference between live (to live) vs live (live event).
I’m not that much farther along in levels than you but I’ve relinquished all doubt in the learning algorithm. You’ll pick it up in rapidly and you’ll just know.
Lets think of it this way. When Japanese people are born, from birth they are learning the language, how to listen and how to speak. They pick it up. By the time they reach school and actually start to learn how to read and write Kanji their vocabulary is quite large. This is the advantage that they have.
The same applies to us. Learinng Kanji first off is not a good idea unless you are complementing it with other lessons to enforce that learning.
The only way to differentiate is to know what the word is. You have an example above and all of those are relatively easy vocabulary words. Seeing the Kanji and knowing what the Kanji means and knowing your vocabulary will instantly trigger in your brain what the reading is meant to be.