Once you've saved your queries, they will be available in the Queries drop-box–under the Queries and Reports section–when targeting mass email or reports. In the queries section on either the include or exclude column, click to see a list of your saved queries and pick one or more to include, just like any other filter. Queries can be combined with other targeting filters as well.
You can also create a new query from the targeting interface if you want. Click the "Save & Create Query" button to save your targeting and go to the query builder. Create a new query and save it to be returned to your targeting page with the query selected.
If targeting an email, you'll be able to view the query you selected from the Preview and Send page. You'll have the option to be taken to the edit page for that query to make any changes.
If targeting a report, you'll be able to view the query in the Targeting tab, edit it, and refresh the report.