What does the areas that I have pointed to do in subtools
The icon on the left is the first of 3 indicating functionality for boolean operations. The one highlighted is union, followed on the right by subtraction and intersection. They only come into effect if you use the boolean function to combine meshes. The default setting is union as you have it here.
The paintbrush icon toggles on or off any polypaint info you may have 
Burchigb,i think thats are some options for boolean operation while extracting and merging subtools.(union,difference,etc)
Thanks was wondering about those areas since they were never explained in the manual or anywhere that I could find