Cool thanks for the help guys. I think scottjl's webdav idea sounds like it'll work the best for what I'm after because:
1. I can leave the NAS exactly how its organised now.
2. No duplication of data across devices.
2. I dont have to use calibre on my whole collection. I use it to convert but not as a library manager, since I find calibre to be extremely NAS unfriendly.
Just need to find a spare iphone to test this out with goodreader
