Personally, I'd prefer to use a custom column, but that is because I already use one for my path/filename. That way I can very easily keep the file structure the same across all my devices (filesystem, sony, and android) I'm a bit of a control freak considering the contents of my SD card...
But. If it's more difficult or fault prone, I'd say go for the first option. The ability to use the content server and wireless connection together (without getting more than one copy of a book in your library) is more important.