Start with it simple just try selecting a folder containing your Videos in the UPnP AV media server not the Root thats alot of work to index in most cases. See if this works first make sure they playback properly adn are a supported media type.
In the UPnP AV Media server settings there is a button to Refresh. What firmware version are you running? 1.01?
As for organizing the folders there aren't any options to change how it is viewed you can basically view it by folder or by all video, photos, or music. I would just create a folder for your Playable Media then have a folder for music, images, and videos. the more basic folder structure the less likely to run into issues indexing.