Core Data is pretty amazing, and I've really enjoyed using the visual layout Xcode provides for it to organize things and get a quick sample of what data I've placed where. At times I've started to wonder if I'm making the best use of it, however, as after a while there tends to be such a mass of arrows that it becomes difficult to tell what's going where.
I try to keep this to a minimum by
but the clutter seems inevitable.
What are some ways you employ to keep it optimally organized and readable?
This is difficult to answer in a general sense. I think it's important and you're right to give this some good consideration. I tend to obsess over the visual arrangement of things myself as I find it has a profound affect on my perception and ongoing understanding of my own schema. Xcode's data modeler is essentially a schema design and design documentation tool.
I strive to compartmentalize my own designs as much as possible. For example, if you consider an iTunes-like case, you might have a controller managing the library source list selection (a playlist, for a simple example), and another managing the members of the selected playlist. In the schema, there may be several "library-related" entities and several "playlist-related" entities, and there are definitely several "song-related" entities (album, artist, and song/track). I'd group the song-related stuff tightly together in a way that nicely arranges the relationship lines, but that keeps these entities visually separated by space from playlist- and library-related items.
In other words, if you keep related items together in clearly-defined logical clusters, separated by nice whitespace, organized in the same way you'd organize your controllers, the concepts are kept fairly clear.
The other problem is Xcode's automatic placement of the relationship lines. Unfortunately, there's little we can do about making those neat. I've been known to spend (actual time redacted out of embarrassment) worrying over balancing clearly-depicted relationships with clearly-depicted clusters of interrelated entities.
Good luck and happy OCD! :-)