If I understand your problem correctly, you're trying to apply a material to a tool that has a texture but are not able to? Textures store their own materials independently of polypainting, so if that is your problem make sure you are using Tool: Texture Map: Fill Mat rather than the polypaint method of Color: Fill Object.
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2) Dyou try posting this to Technical Talk?
Also, are you sure you have separate UV sets?
Textures store their own materials independently of polypainting, so if that is your problem make sure you are using Tool: Texture Map: Fill Mat rather than the polypaint method of Color: Fill Object.