I used to open up a bunch of Konqy windows, some being SU and some not. Then I discovered the "midnight commander" view profile. It's really useful. You automatically have two windows that you can unlink to browse in two separate locations, and you also have a shell down at the bottom so you can SU and do stuff in the commandline without having to actually open a shell.
Check it out. Go to Settings->Load View Profile->MidnightCommander. Quite handy.