What I do is I convert the .3ds file to .x and use a uv mapping program to make a uv map that uses the material colors.It is still one texture but all of the textures make it into the uv map.
Then I export the uv map,make what adjustments I like with a paint program.
I assign the new texture as a bitmap to my model and save the model.
I hope this helps.
There are others in this forum who are better at this than I am so maybe they will pop in to help.
You might also check out the 3Dimensional Chat forum.There are forum members there who can answer your questions about textures, etc.
FLa
Where you can find my demo:http://www.savefile.com/files/6970524