Hey everyone, i gave it a try last night and managed to get several materials on the different subtools it was pretty straight forward really with the help from the community.
import subtools
make sure colorize is turned on in Texture dropdown
import your texture for the subtool
in Texture drop down, do Texture->Color
select your material
make sure you have selected M channel instead of the usual RGB or MRGB
Now paint on your mesh and the subtool that is selected should get the material.
Repeat for every subtool and your done
Hopefully this will help anyone else whos stuck with this!
n-drew, frebel, thanks! i will write a bit about how i did that render with my next update