When you open Custom SQL page, you'll see it looks a lot like the Create New Report one. This page has 2 tabs: Edit and Logs and is divided in two sections: top one is showing the query content (SQL text), and the bottom one lists all available queries. You can also open an SQL Query file that was previously saved by clicking on icon.
 

When creating a new query (New SQL icon), you need to specify its name and click OK. At the bottom part of the page you'll see the query with this name created. Now you can either run a Query builder or write query text in the top part of Edit tab directly. When you're finished with this query hit the save button. Then you can execute it by pressing the Execute SQL button. The Results tab will appear, showing the returned data, arranged according to a certain condition.