Firstly, I would say this is just something that happens naturally over time, even if you don’t dedicate time to studying it specifically. Gradually you will just be able to get a feel for which is which and which ones to use.
There are some things that automatically rule certain things out, though, which can speed up your recognition I guess.
For instance, an onyomi cannot be longer than 2 mora (note that something like しょう is still 2 mora, because しょ is just one mora). So if you see a reading that is 3 mora or longer, it is definitely kunyomi.
Readings that are 2 mora long and end in う or ん are almost always onyomi.
Onyomi originate from a set of Chinese pronunciations, so they tend to be more internally similar to each other than kunyomi readings. There’s really no limit to what could potentially be a kunyomi reading.