figuring out HOW to draw the windows into the texture challenges some people. I still can't get mine to look right, frankly.
have you tried spawning windows along a spline via particles?
if you use 3dsmax, add a spline to the area of the hull where you want windows, create a rectangle the shape of the window (or windows, if you want groupings of 3 or 4), add a particle system and constrain the windows to the spline.
as you add particles, the meshes begin to space out evenly along the spline
render to texture, overlay it to your ship's texture, and voila!