I have found that skin files only work if they are placed at the root theme folder in the App_Themes folder.
For example, if you have 2 themes in the App_Themes folder, you cannot add another sub folder to the theme folder and place a seperate skin file in that subfolder.
It's not much of a limitation, but it would give you more flexibility to further customize an app.
Can anyone shed light on why this behavior occurs as it does in 2.0?