The files in Data\Skins are the original skins shipped with mojoPortal. These skins are updated each time you update mojoPortal. The files in \Data\Sites\1\Skins are the skins that were copied from \Data\Skins when your site was originally built and these are skins that are available to you to set in the Site Settings as the Site Skin. These skins are not updated with mojoPortal updates. You should only edit the files in \Data\Sites\1\Skins.
I have a feeling the reason the changes you have made aren't being reflected has to do with caching. While you are working on your skin, you should turn off caching by either:
Go to Administration > Advanced Tools > Design Tools > Cache Tool and click on "Disable Caching"
Add the following to your user.config file and then "touch" your web.config to restart the web application. (touching the web.config file means opening it, adding a space somewhere and then saving the file)
<add key="CacheCssOnServer" value="false" />
<add key="CacheCssInBrowser" value="false" />