try benoit thornhart's ThemeGenCE
CodePPC - Programmez votre Pocket PC
the interface can be a bit confusing at times but with a bit of trial and error you'll be in full control. it's way way way better than the microsoft one, which does not really support vga devices. ThemeGenCE lets you generate a theme file for any kind of pocket pc screen sizes. it also lets you edit the base hue coloring of wm5 devices.