I've just started to learn Japanese, and I've been looking at the Joyo Kanji. Most of the words have On reading and Kun reading. I was wondering, which one is most popular and when should I use one over the other? Thanks
As a general rule...
There will be times where you'll want to use both ON and KUN readings for numerals in different situations.
For example, when you are counting objects, you might be using KUN readings, like this:
If you were looking at months of the year (January, February, March, etc.) you would most likely be using ON readings, like this:
And do keep in mind that there are a few "weird" numerals (4, 7, and 9) that have their own sets of rules. Sometimes the 4 will be read as し and other times 4 will be read as よん. Sometimes 7 will be read as しち and other times 7 will be read as なな. Sometimes 9 will be read as きゅう other times 9 will be read as く and even other times, 9 will be read even differently (for example, ここのつ for "9 things"; and this can happen for even other numerals! For example: 1, 8, 10, etc.)
As you continue to study, it is helpful to learn both the ON and KUN readings of numerals (even though it is more content to learn) because you will use both, in everyday Japanese.
More information about Japanese numerals can be found on this Wikipedia page, as well.