Yeah you cannot bridge like that, and your words do not make sense: "And when i use the bridge tool to make the hole for the windows it does this". Bridging does not "make" a hole. I would suggest you at least youtube some videos on modeling, textures and maybe some specific tools individually like the bridge tool. Bridge tool is used on open edges [usually] to make the connection between two geometries that are combined but seperate or a hole through a solid geometry to fill the gap between faces. Like if you cut a window hole out of GEO that has an interior "wall" and and exterior "wall", you could use bridge to fill the gap between the interior and exterior effectively making the inner frame of the window. To make the glass to fit into those windows you need to have geometry for them. To make geometry for them can happen several ways. You need to decide how you want the window (glass part) to actually be. Do you want a single pane in the middle of the frame? do you want double pane? If dual pane do you want each pane to be flush with the inner and outer "walls"? Your reference pictures might dictate this, I cannot tell. But ONE way to make the "glass" is before you bridge the inner and outer surface, you select one of the full edges of the window and "Fill Hole", then select that face it created and extract it (or seperate). This gives you the individual glass pane and it is oriented correctly to the angle of the window hole you have cut out. At this point you might want to scale it up just a tad to hide edges and now can figure out if you want thickness, single pane, dual panes or whatever and place the "glass" where you want/need it. Then apply a texture to it.
