Looks like you've reached the advanced features, I'm pretty happy with the learning curve
I had thought about offering a way to clean those parameters but cam to the conclusion this is overcomplicating things; it would be a mess to configure.
With the next release editing all file properties and tags will be possible (almost done). Adding the same tag to multiple files in library view will also be possible, this lets add tags like Serie=IT Crowd, Season=1 manually. Finally I hope someone will create a plugin to do that automatically; I've got enough other things pending :p
These tags can then be used in the name using e.g. '%tag_Serie, Season %tag_Season - %name'
That's right, currently the scan button has to be pressed manually to add new files, watching file changes is a pending feature.
Whe re-entering a folder (e.g. Never Played) it should remove videos having been played; it's working for me. If many files show up in the folder it can take some time (minutes) to refresh. This is because all files up from the first one having changed will first be removed and then the changed ones added. I can't tell why it is taking so long, it's something in the way pms talks with the ps3.
When you click clean library you have to get out of all folders (up to the pms icon in the xmb) and when you enter again the folders should update. Are you using a ps3 or another renderer? Sounds like your refresh doesn't work as with the ps3.