I'm sure this is a really basic question, and I swear I've actually looked through the user manual, but I am missing how to replace citations with numbers during a scan. What I want is for (Doe 2004) to change to (1), then obviously the appropriate reference will be in the bibliography.
This is a function of the format you are using. The settings for such things are kept in the format definition. Please see the section of the User Guide that goes over formats, and if you still have questions post them here.