2. How to undock permanently by default? (all windows).
Open a new project from your regular template "Normal" bu default. Then as above set up your windows choosing undock where neccesary. Make sure the current screenset is unlocked and then "save as" your "Normal" template.
In fact why not go a few steps further and set up a whole bunch of Screensets that suit the way you like to work and then save it as a template. Screensets are a very, very powerful addition to Sonar, new in X1 that when set up can speed up your workflow immensely. They are like the old layouts on steroids. They'll remember all sorts of settings - window placement, zoom levels, track manager states, edit filter states, etc, etc. You name it they'll remember it, just make sure they aren't locked or they 'forget' changes.