Hi,
You can organise your css into a commmon folder as described in this article:
http://www.mojoportal.com/understanding-the-styleconfig-file.aspx
However, I would recommend not putting them in the /Data/skins folder because files are copied from there to the /Data/Sites/[SiteID]/skins folder upon site creation. You could create a different folder like /Data/sharedcss/ or some other custom folder and include the common css files from a single location using the style.config file for the individual site skins.
Hope it helps,
Joe