I would like to add complementary information regarding Part 2 of SpooX's tutorial, about creating the layers with Blender.
My personal recommendation is to group the objects by layers as one would in a classic image processing software. Blender users should be fairly familiar with this. Now, when it comes to rendering, there are 3 main things to set up:
In the Scenes section of the Properties panel (see image below), add as many Render Layers which would correspond to each “layer” that should be brought into Palmer (and which correspond to the ones previously extracted).
For each Render Layer in the Scene section, in the Layer tab, all layers visually involved in the scenes (directly, indirectly, or masking) should be checked in the “Scene” side (left).
For each Render Layer in the Scene section, in the Layer tab, only the layers directly visible in the layer to be imported in Palmer should be checked in the “Layer” side (right), while the others should be checked as Mask Layers.
In the example below, the Scene involves 8 layers, 7 of them to be visibly rendered and one set as mask.
In the compositor (Node editor, icon on the left, Use Nodes ON), add as many Render Layers as defined in the Scene section (Add>Input>Render layer), and set each node to each render layer, as shown in the image above. Likewise, when everything is rendered, all you need to do is to connect a Render Layer node to the composite, save the image, change the Render Layer connected to the composite, save another image and so forth.
Set the transparency for the background of the rendered images. In the Cycles render, it is set by 2 things in the Render section of the Properties panel:
In the Output tab, the output should be switched to RGBA to allow an alpha channel. As far as I recall, that's the only thing to set up with the Blender internal rendering engine.
In the Film tab, the “Transparent” box should be checked.
I hope that helps.