I've seen a few RFEs that suggest it is difficult to know which query is being edited in the query explorer. If you click on a query from the queries pane you will see the selected one is highlighted. Once you click a data item or a filter in the query the highlighting on the query disappears. When working in a report with many queries it can be difficult to keep track of which one you are in at the moment.
There is a simple workaround. Click in the vertical space between the queries pane and the data items box. This automatically navigates to the highest query level properties and highlights the current query.
Thought it would be worth posting in case it helps anyone :-)