@Dawn - They don't really connect. I kept trying to make it work, but I discovered I would need to have a different transport layout for at least 4 different orientations. I was going to build those out, but then the release date for Update 3 was announced and I gave up because using trains will be a much more elegant solution. My plan for Update 3 is to fix all recipe and production line changes to my blueprints and then build train depot blueprints for each factory complex. I'm hoping to get these out as soon as I can, but until I work with and understand the actual train mechanics and all the variables involved I can't give a good timeframe. I hope to be able to participate in the beta so I can expedite these changes/enhancements.
So for now, I recommend connecting them as best you can, with sometimes having a bit of a spaghetti intersection.