The full passage is
> ‘Cut along to the galley. Tell the cook to put all his dirty pans and coppers upside-down. Pullings, Babbington, stop the firing. Boom off, boom off. Back topsails. Mr Dillon, let the starboard watch black their faces in the galley as soon as I have spoken to them.
It is a literal instruction.
The men of the starboard watch are to go to the place where the pans are, the galley, and once there they will use the soot from the bottom of the pans to blacken their faces.