Following mjn's advice, I'd also add a new layer for each texture that deviates from the base. For example, for a Terran ship that is mostly gray but has blue stripes and greebles, I'd have one layer for the stripes and another for the greebles and then superimpose them on top of the base.
An example of my layer hierarchy would be (from highest to lowest):
Glow (for glow maps; optional)
Dirt (for grime, oil, etc)
blue (or whatever color; useful for stripes or secondary color; can also be a texture)
bevel (a style layer that bevels the shapes and lines of the vector layer)
vector (lines, shapes, etc.; can be brushed or vectored)
texture2 (for second texture that deviates from norm)
texture1 (for first texture that deviates from norm)
texture0 (base texture that superimposes its pattern onto the base color)
base/background (the solid base color; usually gray for Terran/Shivan or brown for Vasudan)
R