edit: oops ken posted at the same time I see. sorry
Hey Datman
You know JRiver can't do everything, but some days, it seems like it can.
It is not really clear what you want to do .... you want to start over and do it right okay (there are ways as Ken was saying to do that, including cleaning up your disk directory structure as an example, without redoiing everything)
One thing is to break the habit of grabbing "physical" data. Why set up a system where you have to click on a folder to play it. It is a database, and JRiver gives you so many possibilities, use them.
That being said, a coherent directory structure that is consistent for ripping or importing is great to sort out at the beggining. I think video is easier than audio (or has less choices maybe is better way to put it), as basically if it is a movie its the Name then you have the movie file, a jpg and maybe a sidecar file). All other criteria, generally shoudl be findable,searchable, and filterable from the tag or metadata).
Now for TV you could have a folder for the series, a sub folder for the season. So getting back your "iso" question, to create a new field you will go to Options => Manage Library Fields then add New Field. This would be a User data field. Then you could put iso, 3D whatever in a tag. and create a view using this tag, not a directory where all the files are just dumped.
People can help you with this but think about what you want to see on the screen first, what kind of detail you need etc. once the tag data is available you can then have a lot of options that are not dependant on file structure as Ken pointed out.