this is the higherarchy I use, note that the interior geometry of the cockpit is in a seperate subobject, but the glass is simply glued to the main hull geometry resulting in it becomeing part of the main hull. also, important the glass must use a diferent texture than the rest of the hull, yes I said it has to use another texture, yes this will make it slower than it otherwise would be, no there is currently no way around this, it's a sacrafice you will have to make to get this effect. after you convert go in PCS and make damned sure that the glass texture shows up _after_ the main hull texture(s)
the reasons why all this works is this, the render order of subobjects in FS is subobjects (and then child objects of these subobjects) in the order they are listed in the POF that are first childeren of the main hull one texture at a time, in the order they are listed in the pof, then the main hull one texture at a time in the order they are listed in the POF
now if you get the texture order right, then realy you could get away with havein the cockpit shareing a texture with the hull (wich would be ubber good), but the glass and main hull geometry must be seperate.
now if you wanted something that had fewer requierrments, like say a window on a capship, something were you would never ever have to worry avout seeing other parts of the outside of the ship through the glass, all you have to do is make sure that you gave the texture an alpha chanel and make all the interior geometry is in a seperate subobject.