Place your .dds files in a new folder inside your data/textures folder. In the ck, make a new http://www.creationkit.com/TextureSet. Have a look inside a vanilla one for reference, but basically put your standard .dds file in the top slot and the _n.dds in the next one down (this is from memory so might differ slightly). I think in your case, make sure both "has..." checkboxes are not ticked. Now find the banner object you want to retexture and make a duplicate of it. Double click it to open it up. Next to the "model" line, click the edit button. In the window that opens, double click on the banner model in the list area on the left. Select your TextureSet from the list and your done.
- Hypno