Layers in LDtk can be of various types. Each one support different kind of data. They can be organized from the Layer panel using simple drag and drop.
These layers are grids of Integer values (ie. 1, 2, 3 etc.). Each value is associated with a color and an optional string identifier (for easier access in your code).
You can learn how to use IntGrid layers in this tutorial.
Tile layers contain bitmap images organized in a grid. These layers must be linked to an existing Tileset to work.
You can learn how to use Tile layers in this tutorial.
These layers host Entity instances, which can be placed along the grid or in free mode.
You can learn more about Entities in this article.