How can I find all references to a topic or verse in a number of tools (such as the Journals or Church Fathers)?

Create a User Group (under My Groups) in the Library Panel. with these tools or texts. Then you can amplify to it from a word or phrase to find that topic in all these modules, or click in a verse reference in a Bible text and amplify to the Group to find all references including that verse.

The Group will also appear as an option in the menu of the Research tab so that you can simply search all the fields in that set of modules.

To create the first User Group, select the first module in the lists above, and then choose Add to User Group> New Group from the action menu or the right-click menu.