I just saw this excellent post by sk89q about the various pieces of the Minecraft plugin and modding ecology, and thought, that’s a fantastic way to explain where Lapis sits in the stack!
As shown, the Lapis stack neither touches Forge nor user-space. You place java or lua plugins on top of Lapis, and/or use our own optional vertically-integrated Codex. Also, Commands and Permissions features from Lapis bind down into Sponge to provide basic services for plugins no matter what abstraction they sit on.