Once you've saved your queries, they will be available in the queries filter 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.