Where do I modify the values in the ddrt.properties file so that they will be passed into the exported WAR?

You have to change your perspective to Java (or something that will show the "data" folder). Once that's shown, open the ddrt.properties file and/or the ddlog4j.properties files, update as necessary and save.

When exporting, be sure to uncheck the option to "Reset tracing in the deployed application to the default (disabled) settings" or logging will be disabled.

HTH,
Michael

Another option is to permanently show those hidden-by-default folders without changing perspectives:

1. Click the View Menu button in the title bar of the Speech Navigator view pane.
2. Select Customize View from the drop-down.
3. Uncheck the Hide All Project Data Files option and click OK.

The setting will persist across restarts of OD as well.