Kanji is one of those things that any single way of working doesn't seem to work 100% x-x
There's different methods used in plenty of textbooks. But the biggest issue you'd have is motivation to learn.
My advice is to use different ways and see what works~ you don't have to do all of them, but each has something good to offer.
1. the literal way~
You're given a kanji, it's meaning, reading, stroke order, and that's about it. x-x You're not told how/why/when the reading changes. Kanji power or just Tutle books is one example. This is usually best when learning all the kana. It just takes time.
2. Pictographs~
People say that chinese was derived from pictures, and Japanese was derived from Chinese. Soo they make some kanji like pictures and break it down. They do that so you'd remember/understand the kanji better. Unless you practice writing what you know using it with others, you might eventually forget.
3. Heisig.
This guy is popular for his book "Remembering the kanji" which has 3 volumes. Vol 1 teaches the kanji stroke order, a meaning (might not be correct), and asks you to make a "story" of how it's put together. People criticised this saying that you could learn it in the wrong context, which would make it more difficult. You also have no way to understand how it works together or is read.
Vol 2 focuses on readings, vol 3 is more technical and advanced. (not the normal 2000 kanji)
http://www.saiga-jp.com/kanji_dictionary.html
4. Sentence Mining.
This one i've not tried yet, but it sounds promising~ The idea is that you have a sentence, and take it apart. You learn everything you can about each part, and that supposedly greatly helps you learn. It would cover all the ways to read a given kanji, the particles, etc. The problem with this is that it's more random if you don't have set boundaries, and you may get into something you don't understand. It also means that you're accountable for error, so it would be better to have full material and go from there.
5. Immersion.
This is about surrounding yourself in the language~ it's proven to work since it requires more ways to learn something, and is more enjoyable. This can be things like music, language settings, randomly naming objects, using phrases, etc. You'd naturally start using the language like you've known it forever, which I found useful~
The problem with this is that too much can cause a burnout, or you're likely to not understand/practice what you're immersed in.
6. Practical reading.
This is a powerful way to learn, and is used by alot of university type of material, such as the popular books Nakama, Genki, or "read real japanese." The idea is that you read paragraphs or stories in the language, learn the words in the paragraph and read it again. It's accumulative, so that you get to practice often. There can be a few problems with this~ but they're understandable. The first is that you may get confused about when to use what reading. This can be solved by learning kanji words as vocabulary, rather than a reading. You'll eventually see certain kanji together as a word, instead of one at a time.
7. Practical writing.
This is where you'd go to a language exchange online, write a journal, and native people will correct it. While you'll get plenty of practice trying to use and understand the words, people often won't give explanations.