(works-ish on all iOS, 2.0 through 9.0)
Version 0.9.3919 is effectively just the smallest possible update for iOS 9.
To enable, disable, or change the order of themes, see the WinterBoard panel in the Settings app: there is no standalone app as of version 0.9.3916.
Wallpaper (whether png, html, or any of the other crazy formats that I should never have added to WinterBoard) is not currently supported on iOS after 7 :(.
Give your iPhone, iPad, or iPod Touch a graphical overhaul! WinterBoard provides hooks that let graphics artists safely and simply theme almost anything in Apple's OS, including third party software downloaded from App Store. Multiple theme packages can be installed at once using the configuration interface: simply drag themes into a priority order.
Discussion of WinterBoard itself, including all bug submissions, should be done via IRC: on irc.saurik.com, in the channel #winterboard.
To learn how to use IRC and generally how to report bugs and how to contribute to WinterBoard, see WinterBoard on the iPhoneDevWiki.