I´ve followed this wiki http://guildofwriters.com/wiki/GLSL_Stencilling and have some trouble;
When I try to paint my stencil in 3D view I just seem to access/paint the first layer (the base, topmost in the texture list). It works fine if I select the stencil in UV/Image view, and paint there. It updates on the fly in the 3D view...but it´s quite annoying that I can´t reach/paint on the stencil there. Quite sure I´m missing some basic stuff here (really new to Blender) but I post here if someone know of any wierd stuff like this accuring.
PS. I have checked the Blender GLSL Materials in the Game-menu as well...