If you add the all/all/nopasswd (whatever it actually says) to sudoers (with visudo), then you can add apps that run as root; just preface the commandline with sudo. The xterm, I'm not sure of, but it should be pretty easy.
As far as installing a new version, the control panel plugin will be update the first time you run control panel after the install. You can either reboot, or disable the plugin through "Control Panel" "Panels" then re-enable it. For xterm, the problem is if you start a new xterm with dbus and pass it a command, at least in OS2008, a new terminal opens with no scroll bar, no text, no text entry and the command does not execute. If you try launching the command by executing "osso-xterm ls" or "osso-xterm -e ls" the same thing happens. Ditto for "maemo-invoke osso-xterm.launch" I'm not sure if it worked this way in OS2007, as I have a N810. Does Command Navigator do the same thing for xterm in OS2008? I have looked at the code, and it seems to be using the DBUS method. All the code for xterm and root is in the program, but I commented it out for this version as I did not have enough time to test root, and xterm didn't work at all.