I have the official Apple Color Emoji.ttc. I want to use Glyphs 3 to replace few glyphs in this font. But when I’m trying to do this, there are lots of layers in different size. What’s is the best way to replace glyph in official font? I’m planing to use this font as a system one (Mac OS X).
What exactly are you trying to achieve? Messing with the system font might lead to confusion as you would see something else than everyone else.
Said that, you need to produce images for all the sizes and replace them. You could just overwrite the .png files that you find next to the .glyphs file.