You can use color in an AO-texture. Just understand that full white allows the original underlying color to pass through fully, where black fully blocks it. So when having some pixels as 'red' in an AO map, it will essentially only allow the red channel of the texture underneath to pass through. The technique can be used in a limited way though, since you can't paint/overlay white colors this way. It is however perfect for darkening areas of a model, or even tuning the colors a bit (due to light sources or whatever).
For adding text to a specific place on a ship, I recommend using decals. This is a simply geometric flat mesh, positioned close to the side of a wall for instance, and then you put a (transparent) texture on it. But you'll need a 3D program to create that mesh though.
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