With logic.

Parts of a texture are going to use same materials, unless your skinning a Chimera or something.

In photoshop, just make layers for certain materials, don't completely section everything off into chunks of "barrel" "handle" "button" "bolt" etc, this makes it way harder to make things look seamless. Same goes for forerunner textures, or anything else for that matter. You can just do a base layer, overlay the bump map or shape layers onto it with a high pass filter on it, and then just build up layers on top of those using the selection tools and the paint brush tool to build up layers of detail and give them different blending modes.