Layers

If you don't use layers, the layer options can be ignored (changing them will result in no changes). If you use the plugins in CMYK color mode, the layers options can be used, to control the black channel values.

Create a new layer, either by duplicating the existing layer or creating a new layer via layer menu and then adding something to the layer (below it is a gradient)

Apply effect (Patch plugin in this case applied to the gradient layer with no modification to the settings).You will see will see areas of transparency. Click the advanced button.

On clicking the advanced button you will see a dropdown marked 'Layer Selection'. Select this and set the dropdown to inverse red (this means the transparency information is based on the effect's red channel and then inverted). A number of dropdown options are available such as gradient transparency, diagonal transparency and others. Each option varies (in some way, subtle or otherwise) the transparency.

Apply the effect and you will notice the changes to the layer / trasparency. The layer can now be manipulated further such as applying layer effects or transforming the layer or adding or subtracting from the layer

In the case below, one of the default styles was applied to the layer. Any style can be applied, or just add a drop shadow or gradient or a stroke to the layer. The layer's blending mode can also be modified and more (please consult the Photoshop manual for the huge range of possible layer uses)

As with all plugins, the previously modified layer can be re-used as well as layering multiple layers / plugin effects.