Ahruman, i'm currently drawing out an effects map for the hull 'lights', have i got this right:-
blue = laser heat
green = hull heat
red = engine power
so my effects map needs to be painted red on black so that the glow effect is tied into the engine power?
Not really. :-) The Shady Cobra shader expects red = engine power, green = laser heat, blue = illumination. Hull heat is constant over the ship.
The “illumination” one is limited, though. It’s like casting white light on the surface, which isn’t useful for your red and green lights. Ideally, for your design, you’d have three textures: one base, which is the ship with all the lights off; one permanent glow map, which is a full RGB texture for the red and green lights which I assume are on all the time, and the third with the engine-related glows. This could either be RGB (for maximum flexibility) or a single channel specifying intensity, with preselected hue. (Making the most intense parts whiter is quite easy.)
If you do a single channel, the other channels could be used for, say, laser heat (intensity specifies how much each part of the ship is heated by the laser, and the shader selects a colour based on temperature, as with the Shady Cobra) and a shininess map (0 means matte, 100% means very shiny).