Well, there are two things to consider:
Most nodes, that you work with in Godot inherit Node2D or Control, which both inherit CanvasItem. This node has has a property z_index, which defines the position in the z axis, or in the depth of the canvas if you will. So this
Node 1 - z_index 1
Node 2 - z_index 0
will lead to Node2 being drawn above Node1, although the order in the scene tree is the opposite. However, it's best to use these only when necessary, because by default, nodes will be drawn the order you put them in the scene tree.