The link on this page is a big Photoshop file.
It is the template I used for my WB skins (specifically in this case 'Cubano') which I've decided to share with you. You can use it as a reference, as a tutorial, take it apart, change it - do whatever you like with it... (but don't post a duplicate 'Cubano' please!)
There isn't a single way to design a WB skin, but in my later designs I worked from a single PS file containing folders of layers for each of the elements of a skin. It may not be 100% complete - I don't think my skins ever were - but all the essential bits are catered for.
My process was to work on this PS file until I'd prepared all the elements for the skin, then turn off the backgrounds until the element was against transparency and then slice it out into it's own image file and save as a .TGA The next bit was to put it all together using SkinStudio (although, and this may surprise people, I never used it - I always edited the UIS files manually).
If you open this file (it probably needs PS3 or above) you'll find that the folder of layers are coloured - purple for the window body, orange for 'XP' related, yellow for mockup-ups and backgrounds (just to see what it would look like), grey for unused stuff (maybe I just wanted it there for a reference), and most of the green being the skin elements. Hopefully the layers and folders are named sensibly. Turn the folders on and off... open the folders... turn the layers on and off and see what they do... take a peek at the layer styles and effects... play around with it.
Like I say - every designer does it their own way, and I've not had any PS training so it's just how I do it.
I hope it helps any budding skinners...