How do I pass kern info to layered-color instances?

I’m making a font that this tutorial calls a layered color font:
For clarity for the designer, I made a total of three instances: two for colors, and one with both the components together, for him to use first. On this combined instance, I set kerning to my satisfaction. I then generated the two other instances, and was surprised to see that not only did they not inherit the kerning information, but when I set the kerning information for a color instance, it erased from the combined instance!
How can I set the kerning for all three instances at a time? Do I use kerning groups? Aren’t kerning groups limited to glyphs within one instance?

Groups are font wide. Kerning values are stored per master. You can select all kerning values in the kerning window, then copy and paste the kerning from one master to another. Switch between masters with cmd-1,2,3,…

When you switch masters, you never should use the layer panel. Only use the toolbar icons and or, as mekkablue said, use the keyboard shortcuts: cmd+1, 2, 3.
And for layer fonts, the kerning of all masters has to be the same. So you keen the first master and then copy the values to the other masters (again as writen above)

I’ll just let this sit here as a warning for future readers: a two-color font is something only a Glyphs whiz-kid should try. It’s a terrible choice for a first font! I eventually had to subcontract it.