Am I doing something wrong, because auto-arrange just isn’t working for me. I’ve got six parts that I can easily place manually on the bed, but if I drop those six parts randomly and auto arrange it wants to split them onto two plates! I’ve tried reducing the spacing and unchecking Avoid extrusion calibration region, but still no good.
I doubt you are doing anything wrong. Auto-arrange is not very intelligent. It often puts object near the edge off the plate for no reason. It does other strange things. For anything other than to move a couple of object to an okay location you will probably have to do it manually.
The other issue, which you did not mention is whether you have sequential printing enabled. If objects are going to be printed sequentially it tries to account for the print-head size, the height of the carbon rods and it will often think that it needs object much farther apart than you would think they need to be. I have overridden the layout many times by setting the size of the print-head to 0 and manually arranging objects.