[whpalmer4]

I'm not really sure from your description what your desired diagram might look like, but I wouldn't give up so quickly just because the automatic layout can't handle an arbitrary graph. If you link the objects with lines (click on the line tool, click on first object until it pulses, click on second object) you can drag the objects around as if connected by rubber bands, and you may find that it is not very difficult to get a polished result. You may also be able to start with a hierarchical version to get the basic automatic layout, then switch it off and add your extra connections. It's worth some time experimenting, and you'll want to spend a bunch of time experimenting anyhow if you're going to acquire any fluency with the app!