I have created a module to hold documents with a relationship to Opportunities.
I have also added a relationship from the built-in "Documents" to Opportunities.

When trying to attach documents to an Email only the built-in "Documents" are visible. I can not seem to adjust this via Studio.

In the Email attach from Studio window, can I customize that search window to search/filter by Opportunities? Or is it possible to link the Email Attach button to a new module which I can have custom search/filter options?