Most of the 3D channel effects create mattes, which are ( grayscale images in which black represents transparent pixels, gray represents partially transparent pixels, and white represents opaque pixels). You can then use these images as track mattes that hide parts of the 3D data and reveal other parts of it.
Say you import a 3D animation of a car moving towards the camera. You'd like to insert a 2D image of some smoke halfway through the car's journey, so that it starts behind the smoke, drives through it and ends in front of the smoke.
To achieve this effect, you'd apply a 3D channel effect like 3D Channel Extract to the car layer. Then you'd click with your mouse at the point where you want the smoke to appear (halfway back into the scene). After clicking, you can read the Z position of this point in the Info Palette.
Adjust the Black Point and White Point properties in the 3D Channel Extract effect properties, until you get a matte in which the white starts where you want the fire to begin and ends at the camera. Everything behind the fire line should be black.
Arrange your Timeline with the layers stacked from top to bottom as follows : matte layer, copy of original car layer, smoke layer, and another copy of the car layer. Notice that the matte layer was made with a copy of the car layer, so the car layer will appear three times in the comp). Use the matte layer as a luma matte for the layer immediately below it.
In the comp, it will appear as if the car is passing through the smoke.