Creating a Skin documentation is here: http://www.mojoportal.com/creatingskins.aspx.
I think what you are wanting is to create your skin and force the site to use it. To do that, use the guide mentioned above to create the skin and then upload that skin to the \Data\Sites\[1]\Skins where the [1] is the ID of the site you want to use the skin on. After uploading, go to the Site Settings and select your skin.
If you want to change the default initial skin for a fresh installation, find the key below in the web.config file and set it's value to the name of the skin that you want to be the default for new installations. After a site is installed and this key was set during that install, it's skin will be styleshout-refresh.
<add key="DefaultInitialSkin" value="styleshout-refresh" />
Hope this helps,
Joe