When you learn the kanji, do you specifically try to remember “this is the kunyomi, that is the onyomi?” If so, how do you keep them straight, and why is it important?
I didn’t pay any attention to it for the first few levels, and I’m wondering if I messed myself up.
Over time you will just start to get a feel for which ones are which. There are some restrictions on each that eliminate certain possibilities, so as you gain experience, you will just notice that kind of thing subconsciously.
For instance, any reading that is longer than 2 mora is going to be kun. Readings that end with ん are almost always on. And other such rules of thumb.
Huh. I was kind of expecting you to say the usual “even native speakers don’t learn which reading is which until grade three at school.” 
even native speakers don’t learn which reading is which until grade three at school
Gotcha. Thank you!
It doesn’t really matter. There are some rules (with exceptions) like “body parts use kunyomi” so you know that 足首 (foot neck → ankle) is read あしくび instead of そくしゅ, but I think it makes more sense to learn that with the vocabulary than to learn if something is on or kunyomi.
Also, what @Leebo said,
I don’t care anymore since there’s a lot of exception to that rule 
It’s important to get the vocabulary reading right than to memorize the rule which would disappoint you in the long run 
It’s not so important to memorize which is which. It’s much more difficult to learn kanji that way, as opposed to learning vocabulary, and then extrapolating backwards. In general though, the on-yomi tends to be used more due to it being the preferred reading for kanji compound words, so if you were to focus on one, in most cases I would recommend memorizing the on-yomi.
That’s how I do it and it seems to work for me. I used to want to achieve the impossible goal of memorizing every reading of every kanji, but realized it’s not an achievable goal. Learning words individually by their reading, and associating that with kanji I already know seems like the best way to learn these. Over time you learn to recognize some patterns and are able to intuitively read words you don’t know, and even try to guess the meaning (but that’s a 50/50 chance of getting it right even if you know the meaning of every kanji)
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