If the module selector (above the new and delete buttons) doesn't have anything in it, then root-portal has been unable to find it's modules. Try running with the -v option (verbose) to see where it is looking for modules.
Once running if you have closed the config window there are a few ways to get it back (without restarting). If you have any gnometext windows, right-clicking on them should bring up a menu with the option "Configure" in it. Running a second copy of root-portal will signal the first to display its config window. You can also send root-portal SIGUSR2 to display it ("killall -12 root-portal").