Hi Kym Jackway,
Concerning #1, yes this is possible within the diagram manager. The ducts themselves are polygon features, so they can be reshaped into squares. Please see Creating square ducts on a UFMWall for a little more detail, especially the replies in this chain. In short, you can certainly create many shapes and save them as duct bank favorites for reuse.
Now, within the Conduit Configuration dialog, the ducts will still look like circles. Typically, GIS folks are working with this dialog and field folks need the butterfly diagrams in order to visualize the manhole or other structure. So your butterfly prints for the crew will have circles and squares, but this behind the scenes conduit dialog will still have all circles.
For #2, you are correct that this is not out-of-the-box behavior, so I defer to others to chime in on this possibility.