Per Application rules will show up eventually, but I'm holding off on it because they're essentially a kludge. That being said they will show up eventually.
At this time you can use an add-on utility for you window manager (compiz has a window rules plugin for example) to set the xpad windows as skip_taskbar.
Another option is to enable grouping (if you're using 0.3.9).
What might be the most correct option (I'm not familiar with xpad) would be an skip_tasklist configuration option in the program itself.