You can resave and then upload to the Portal/0/skins/skinname folder and then Portals/1/skins/skinname folder - then each portal will see only the skin in that portal. That is called 'localised skinning' - or 'per portal' skinning.
If you have skins in the _default/skins/skinname folder - then every portal that resides in that install can see it. That's regarded as 'global' skinning. It's shared amongst sites and everyone can see them.
You can programattically do some things, but this is the simplest, quickest approach.