Needs to be done in prefs in a consistent way that guarntees it carries over across updates. Privoxy needs to be configured to filter access and so on.
Via its localhost interface.
Since on the WS it will go thru Tor.
I2P comes with applications that are not easy/possible to separate from the node itself at the moment. Also tunneling thru Tor gives more protection in case the nodes are rogue or they are installed on spyware friendly systems like Windows.