I used to use the auto layouts feature in OmniGraffle standard version 5 and within its inspector there was an option for Selected Object Rank, to guide where nodes would appear in relation to each other. Since upgrading to version 6 this option doesn’t seem to be in the same place anymore alongside the other auto layout options.
Has it changed to a different tab in the new UI? As I can’t imagine it would make sense for such an essential part of the auto layout system to have been removed.
Sorry for the inconvenience! It looks like you’re encountering a known bug that was in OmniGraffle 6.2. The good news is we’ve remedied it in OmniGraffle 6.2.1, which was released April 14th. If you check for updates, that should get you up and running with a version of the app that includes those directional controls again.