Hi Gene,
Basically, you just need to select your use cases in the main list view using multi-select techniques (Ctrl+click to select individual items, or Shift+click to select a range). Then run the report with that option selected. Where you might run into problems is when the main loop of the report doesn't match the type of selected items you give to the report. For example, the Project Specification report loops through all the packages. If you tell that report to run against selected use cases, it will look for packages in the selected items, and not finding any, will generate an empty report.
Not sure if this is the problem you are running into. If not, feel free to send us your custom report and we can take a look to see what the problem might be (note that these forums are public, so please open a support ticket if you want to keep the report private).