I've been usinfg this fora few months now it's good also got a really good remote control app on my HTC desire.
I am not an expert so can't offer any major advice, but as folder structure goes, if you create a TV Shows and Movies folder within your public videos folder it will automatically pick them up when you select tv shows menu or movies!.
Each TV show needs a folder of it's own then under that a folder for each season
eg. TV Shows>Sopranos>Season 1>
Same for movies and music. If you choose to kepp you files outside the public folders you will have to add them manually from the add source option.
Hope that helps.
One thing I found the other day is that you don't have to unzipvideo files for it to play them either it will play them directly from the zipped archive, which saves some hassle.
You can also turn on hardware graphics acceleration so your graphics does all the hardwork encoding the video, this is the main reason I started using it so I didn't need to update my media centre which only has a Pentium 4 processor and couldn't handle 1080 MKV files.
If your looking for a beginners guide for using it try the wiki pages rather than the forum if I remeber rightly I think there was a beginners guide on there. I found once I sussed the file structure out everything kinda dropped into place by just trying stuff out.
If anyone has any questions I'll do my best to help but I am no expert