Create new skin folder
In the YourMagentoDir/app/design/frontend/default directory create a new folder "NewSkin". For the beginning you can simply duplicate your main skin and rename folder to "NewSkin".
How to change the skin around the one store view
Go to Backend->System->Configuration->Design->Themes Tab, change store view and set "Skin (Images / CSS)" field to NewSkin value.
How to change the skin around the store
Go to Backend->System->Configuration->Design->Themes Tab and set "Skin (Images / CSS)" field to NewSkin value.