First I used http://www.javadecompilers.com/apk to decompile my apk and I found what I wanted to modify, but I couldn't find an easy way to recompile the apk after the modifications. So I used apktool to decompile my apk because it has a handy build feature.
The problem is once I decompiled instead of getting .java files, I got a lot of .so files. How can I further decompile these .so files, or perhaps how can I recompile an apk from the website I used?
Or perhaps a better method to decompile, modify, and recompile.
You can use Apktool https://ibotpeaches.github.io/Apktool/ to Decompile your apk. Then modify codes in ClassName.smali You can recompile the modified files to apk using apktool. (Note : Need to sign the apk so that it will be installed on the device).
->But upto my knowledge till there is no decompiler to decompile .so files.