On’yomi are only ever one or two mora. Other than that guideline you’re probably better off just picking up the pattern as you go. But if you’re really curious now, this stack exchange question has some good information. The references in the second answer will probably be most useful.
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I have not a single idea which readings are kun or on, I mean I know kun is Japanese and on is Chinese but I couldn’t classify all the readings I know. I just rather going with the feeling than going through the whole thought process of “one kanji word” → kun reading → (kun reading of the kanji), and after a while it gets intuitive.
I also do this but intuitively. I don’t think that knowing which are kun and which are on is necessary to do this, but it certainly helps some people.
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If someone is doing that, they know the onyomi for those. Kanji don’t have phonetic components for kunyomi.
I also tend to remember which is which naturally, and I do find it helpful.
But I also study Chinese, which probably makes it more intuitive which are onyomi, and also makes it more of a helpful thing to know, since remembering onyomi in Japanese helps me remember the Chinese pronunciation of that character.
Yes, indeed, I can not purposely think of using the on yomi reading without knowing which one is the on yomi reading, I thought that was fairly obvious.
What I meant, which I thought could be deduced but apparently I might have to spell it out, is that I can tell when a kanji is being used as a phonetic mark and can intuit which of the readings is the one that gets used in such cases (even if I didn’t know that on yomi readings were used and I didn’t know which was the on reading and which was the kun reading).
But now, since it’s been pointed out here that the on-yomi reading is always used in this case, I will be able to deduce it for certain kanji. 
I guess I mean, the names are less important to the question than the distinction of the two concepts. If someone understands all the ways they are different and thinks about them in that way then I’d say they “differentiate onyomi and kunyomi” whether they can explain it or not.
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