Automatic layout difficulties
 

Unlike what others have been asking, I'm not trying to turn auto-alignment off, but for some kind of settings that allow it to:
(a) keep the objects within the page layouts (as opposed to coming together in a blob that leaves the ends of my document empty east and west, and spills over it north and south);
(b) takes some account of the starting positions (as opposed to utterly arbitrary ones that have items in opposite corners from where I want them)... is there a way?

Sorry, neither of these behaviors are currently possible in OmniGraffle.

We've existing requests for both of these in our database; I've added your comments to them.

Depending on your situation, you can apply automatic layout to a selection of objects by using Arrange → Diagram Layout → Lay Out Selection. So creating your chart with Auto Layout off, then selecting only objects that are of lower rank might help.

If anyone else is interested in seeing this, feel free to write in to [email]OmniGraffle@omnigroup.com[/email] and we can add your comments to the feature requests!