This is a short description on how I usually skin my characters with SoD.
After I created the bones, I select the object and start SoD. It applies the SkinModifer, then I add all the bones and reset them.
First, I create the SkinShapes for the bones. I already have a small library of SkinShapes which I just load in, so I will have a rough skinning after a few seconds. Fixing SkinShapes that do not match correctly is also done pretty quickly.
In general, you would setup the SkinShapes the same way as skins envelopes, but they are more flexible because you can deform the SkinShapes in any way. Overlapping SkinShapes share their weights, but there will be no smooth transition.
Now, the real skinning begins...
I usually start with the EdgeWeightTool, because it is very fast at skinning larger areas. Creating the transitions between bones is working great this way. I skin from the outside to the inside, this means I first skin the feet, legs, hands, arms and head, then I go for the hips, spine and shoulders. Toes, fingers and face are the last.
The VertexTools are good when it comes to fixing difficult areas like the hips and shoulders and to cleanup the weighting. Also, I usually create some SelectionSets to quickly hide different parts of the mesh to get access to all areas.
The last step would be the skinning of muscles. I use the EdgeWeightTool again for this, because most muscle definitions are along edgeloops, which makes weighting them very easy. This also works well for skinning clothes.

And that's it, the character is ready for animation :)