Firstly, try never to use subtract, it will always cause you more harm than good. If you want a patch in the middle of the wall that is a different texture, you could make a very thin brush and have it sitting ontop (be sure to make the brush 'detail'), but the nicer solution would be to have it in line with the wall, and remake the wall to be four (or so) brushes which fit around the new bit.
Oh and pipes are made from 'Patches', which are basically single sided objects that can be curved. in the menu you can create basic flat patches or cylindrical ones, the latter is what you'll use for your pipes.