Just need to update configuration settings:

Inside System->Configuration->General->Design->Theme

Set same values for each store view.

Just need to update configuration settings:

Inside System->Configuration->General->Design->Theme

Set same values for each store view.

Added :

As you said need different files for each stores also. So you can do this way:

1. Create copy of theme folders inside design & skin folders. Ex. rwd_store1 & rwd_store2
2. Now follow the same way set those themes as per store in configuration.

Feel free to upvote if helped. :)