This tutorial is for Paint Shop Pro.
If you use PhotoShop, please read Dalriada's tutorial.
Adding a transparancy isn't as difficult as it first sounds.
The trick is getting the right RGB for the transparent parts. Using a light colour will work for light skintones but will show up against darker skintones in-world and in stylemaker. Using a very dark colour would have the opposite effect.
Through much trial and error, I have found that the RGB values of 107,82,57 works across all the skintones in There.com. The values represent the Chocolate skintone, so be careful when previewing to NOT use that skintone in stylemaker or anywhere on your design that you do not want to be transparent.
Working from the wireframe created with stylemaker, create a new layer and flood fill with the chocolate (107,82,57) colour. You can turn the visability of this layer down so that the wireframe shows through while you work.
It's also a good idea to include the figleaf as a layer, for the minimum coverage requirements, so do that next.
You should now have the basis for your design. 3 layers with the figleaf on top, a solid block of colour in the middle and the wireframe partially showing through.
Anything you do from now on, do on other layers so as not to disturb the foundations you have created.
When you are ready to test your design with the transparency, turn the visability of the transparency layer up to full.
Merge all the layers and/or convert the image to 256 colour/8bit. Do not use dither or error difusion as this will ruin the design.
Save the image as a .png file.
You can preview the file now. Providing you are not using the chocolate skintone in stylemaker, you will see the area(s) that will become transparent.
Using the colour picker/eye dropper, set the background tool colour to the chocolate fill.
Set the image/pallete transparency to the background tool colour and re-save the image.
Switch over to stylemaker and press F5.
Lo and behold, the chocolate has gone and the skintone is now showing through. 
If you are still struggling to figure it out, take a look at the example file (compressed zip):
http://thumdar.com/images/stories/library/transparent-dalriada-davesmeg-thumdar.zip
There are samples for both PSP and PS, as well as a screen grab of the design in stylemaker with Caramel skintone.
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