On upgrades, the new versions of skins will be updated under /Data/skins, but we do not touch the skins already in the site specific folder /Data/Sites/1/skins/ in case you have modified them without changing the names.
Note also that a new release of mojoPortal is coming today, version 126.96.36.199 and I have done a lot of work to re-organize the css selectors in the style.css file to make it easier to find what you are looking for. The new release is actually already posted on our Novell Forge download page, I am uploading to Codeplex now and working on release notes. So if you are starting a new skin, getting the very latest version will give you skins that are easier to understand and work with. You can copy them form /Data/skins to /Data/Sites/1/skins but be carefu not to overwrite a skin you already modified.
Hope it helps,