Fixed in latest release! There are a few things that had to be tweaked; namely the selection boxes are rather large and not shifted to reflect the placement of underground pipes, as well as there is no way of telling what kind of pipe it is just by the shape of the fluidbox visualization. As such, I have added a new feature: underground pipe opacity. Underground pipes will show up with a configurable opacity value, so you can see them better. Ducts have a separate setting, in case you wish to just see those.
If you wish for me to shrink the selection boxes more, let me know! That's not super hard to do.