Do I know all of them? I'm going to make a quick test. I'm going to find a list of phrasal verbs somewhere, and "sample" and see how many I know of the first twenty on the list. You'll sort of have to trust me... By "know," I mean that if you showed me the meaning and the verb, I would give the correct preposition instantly and without thinking. Here's one such list: https://www.englishclub.com/vocabulary/phrasal-verbs-list.htm The answer is: 20 out of 20, no doubt at all.

We may not know all of them, but we know most of them because we grew up hearing and using them, the same way a native Spanish speaker absorbs which nouns are feminine and which are masculine.

but to answer your question yes, we know them all, it all just depends on context. when you understand the context you will understand how the phrasal verbs work

it is something you will learn with practice and speaking english, just as everyone else has said, it is not that we go around memorizing things in school but that we are familiar with the language to the extent that we know what sounds right and what does not.

Because native English speakers hear them being used every day of our lives right from being babies. The key with phrasal verbs is context, and because we hear them used by people around us when we are children it just becomes intuitive why and when to use a certain preposition with a verb. We do not learn them at school, and no ever thinks "oh, should I say pick up, or pick at, or pick on," we have simply heard them so many times in context that it is just natural to use whichever one is correct for the situation. It's the same reason why native Spanish speakers understand when to use the subjunctive instead of the indicative tense, you are immersed in the language and it just becomes second nature to you.. Not so easy for a learner who hasn't been brought up surrounded by the language.