You should be able to control URDD no matter if you start it from the web or from the console. Starting it from the web interface could be a rights issue (or your user is not admin). Or do you happen to have multiple installations at the same time.
I'm still experimenting with URD, as I'm not sure it's the solution for me yet, so I'm ok with how it's running right now.
Only 1 installation, and my username is not admin.
One thing I do not see, is way to automagically sort downloads.
My current set up is CouchPotato & Sickbeard scrape NZB's and feed the nzb's to Sabnzbd with category info attached. Sab then downloads everything into diffrent folders according to category & in the case of TV shows the show name & season folder. For movies it's just the movie name.
I'd like something like this for URD as well. I know that URD supports scanning a folder for nzb's, and that would work fine. But I need the categorization & renaming abilities that Sab has for my current set up. Otherwise I may have to limit URD to building nzb's for Sab until URD has a, for me, more complete feature set.