I’m only up to level 5 but I notice many kanji have secondary or tertiary meanings like 本 can mean book, origin, real, main. Since I always respond with “book” when I see this kanji in the SRS I feel like I will forget the other meanings.
What are good methods for memorising all the meanings?
Short answer: through vocab.
I don’t remember meanings of many kanji by now, only how they are used in vocab.
You’ll see vocabs that utilize each of the meanings, like 本屋 for the “book” meaning or 本館 for the “main” meaning. So you’ll have to learn all the meanings sooner or later anyways 
don’t worry about it…just go with whichever one sticks (even if you can never remember the primary meaning). eventually as you learn new vocab the concepts a kanji represents will start to make more sense, and your understanding of its meaning will change anyway.
at this stage the main goal is to recognise the kanji exists and build a crude framework which you can refine and fill in the gaps later.
You could also try not just entering the one meaning but trying to switch between them (beware that you might get them wrong more often that way) or at least try to recall the other meanings in your head or say them out loud.
There’s also a userscript ([UserScript] WaniKani Fast Abridged Wrong/Multiple Answer) which shows all the meanings automatically even when you get it right.
I honestly think this is how most native speakers handle it. That’s certainly how it is for me in Chinese, anyhow. Each common phrase is like a sort of ‘mini-context’ for me to remember a particular meaning.
@chrisarrow I also try to remember (or have learnt, through experience) a ‘main’ or ‘original’ meaning for each kanji from which almost all the other meanings can be deduced. However, some meanings are just so different they might as well be for another kanji. (In the case of 本, I’d say – ironically – that ‘book’ is actually the odd one out.) When that happens… I tend to make up a link? For instance, a ‘book’ is a sort of… underlying substrate on which to write? Sounds similar to ‘origin’. (It helps that in Japanese, unlike in Chinese, 本 is also read もと, a word that itself can mean ‘foundation’, which is essentially what a book is for writing.) I mean, there probably was a link originally, or that meaning wouldn’t have been assigned through evolution.
Either way though, usually other meanings will only stick with exposure and real-life practice (that includes reading and listening with understanding), so don’t worry about it too much. I think @JuiceS’s script sounds like a good idea, but nothing beats repeated exposure in context, because that will make the word more meaningful to you.
I just realized I’ve been worrying a bit about this as well. Mostly because I tend to choose one of the offered meanings that I feel will “stick”, and then I just ignore the others.
In the beginning, I made more of an effort to use different answers to the meaning during reviews. Now, I stick to one of them that I know I’ll get right. ^^;
I do understand that reading more in Japanese will fix the issue. Still, I’m worried about the kanji with alternative meanings that are seemingly at odds or just very different from each other. I do worry a bit about whether I’ll choose the right meaning when meeting them in the wild.
I guess, I’ll find out.
I will be impressed if you ever find yourself in a situation where you need to choose the right kanji meaning in the wild 
more likely you’ll come across a word you don’t know and you’ll have to look up the meaning anyway 
I guess you’re right. Still it would be nice to nail the meaning.
I still think meaning is the wrong word…something like concept is probably better
I think 本 is the only one to which I respond with “book”, since 元 means “origin” as well and I don’t want to confuse them. I guess the 本 in 本気 is closer to the meaning of 本. As @Jonapedia mentioned, “book” is not the main meaning. I’m also not particularly fond of the kunyomi reading もと, unless it’s a part of a name, like 山本.
For new kanji I go to jisho.org, look up all meanings and from that I try to build the core “emotional” meaning of a kanji, which covers all of the contextual meanings as well. For me that has worked so far. For instance, 生 means “life”, even in a word like 先生.
Also, exposure to vocab is a great idea. WaniKani offers a couple of words, but one can find more in dictionaries, too :).
Sounds like what I do. 
I guess so, though you have to make the link between ‘life’ and ‘new life’/‘coming to life’ (i.e. birth). Lateral thinking is very useful for understanding kanji.
Ah, you’re completely right! In 生む and 生まれる, for instance, right?
Yup, for example. 先生 draws its meaning from those senses: someone born before you is worthy of your respect, or so the logic goes. In Chinese, 先生 is how you say ‘Mister’, so it’s polite there as well.
EDIT: Apparently it works as a word for ‘teacher’ too. That’s the first definition in my Chinese dictionary. I haven’t heard that usage in contemporary Chinese though. In period dramas though… possibly.
Hmm I feel this “teacher” thing is more of a general term, in line with “someone born before you is worthy of your respect” as you wrote. it’s often used to refer to mangakas and I heard it used for doctors in anime as well, but in a more respectful tone and not to emphasize someone’s profession.
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