I'm not sure what the exact question is, but i'll give some general hints. Maybe they help...
jPCT's file importers load either the texture or the diffuse color of a material. They don't load both. So once you assign a texture to a polygon, this will be taken instead of the material's color.
Before the first rendering, the object will be compiled. After that, you can still change the textures but what should become an individual texture can only do so if it was one before compilation. An example: A six sided cube that had the same texture on all sides can't be changed in a way that each side gets its own texture. If you want that, you have to assign an individual texture to each side before the compilation happens.