if you are using the Portable MB verison, only the Skins sub-folder where MB is installed is used.
if you are using the Desktop or Store MB verison, the Skins sub-folder where MB is installed is used as first priority. Because that folder is not writable, MB also checks Users/My/AppData/Roaming/MusicBee/Skins.
If the same skin name is detected, MB should use the one with the latest modification date