yes, but I mean not only the phasers... the sensor (thruster?) pods are actually painted over the *hull*.
what I mean is, cut those modules away, and paint the entire plating alone, and paint the sensors over in another place, or another file altogether.
use Unwrap UVW instead of UVW Mapping, and do cut the mesh into different objects (assuming you won't be doing any further modelling over it.... otherwise you'll be doing twice the work), or assign different material IDs.