Designate a Reference Target Window
Normally when you click a blue Bible cross reference in an e-book your Preferred Bible will jump there. You can however "override" the Preferred Bible making a different Bible look up the passage. Open your desired "look up" Bible. On its toolbar click the Reference Target icon. Now when you click a cross reference this Bible jumps to the location. You can also designate a commentary as the Reference Target to make it look up the verse!