Does this mean that If I want the flexibility of choosing from 60 skins among all sites within the instance that a copy of all 60 skins must be kept up to date within the \Data\Sites\%number\skins folder of every site?
Yes, this is how mojoPortal works. But I'd recommend that you identify a small subset of skins that you will be using for each site, and just keep those under each site's skin directory. The reason is that when you upgrade mojoPortal, you will also need to update the delivered skins under each \Data\Sites\#\Skins directory, to incorporate the necessary CSS changes. The easiest way to do this is to copy them down again from the \Data\Skins directory following the upgrade.
Jamie