You have differents type of "effects". In Smode, we call them "Modifiers".
You have 3D modifiers that can be applied on 3D layers, and 2D modifiers for the 2D layers.
Note that a Compositions is a 2D layers which can contains 3D Layers.
You 3D layer can have different renderers: Point, Lines or Suface. Each of them work with 2D layer too. So you can add a composition as renderer.
If you wan't to applied a shader as surface:
you can simply change the type of the layer inside the default surface and follow the instruction of the mentionned tutorial.
If you wan't to apply a 2D modifier over some 3D layer, without affecting the rest of the compositions:
Best way is to put your 3D layer inside another composition (select them and Cttrl+Shift+C) that use the same camera and put your 2d modifiers over this new (sub)Composition.
Beware: It might create weird perspective and depth effect, depending of the order of your layers.
Hope it's help