Yes, this is functionality which Deski 6.5 Users may not be aware of in Webi.

When you are in the Edit Query Window, you will notice that on the left-hand pane there are 2 tabs, by default you are probably in the Data tab, holding the Universe objects ready for you to drag into your query.

If you change to the Properties Tab and then scroll down you will find a Prompt Order section which display all the Prompts referenced by your query(ies), with move up and move down arrows which allow you to change the order.

Once the query has been run and the report has been saved then this Prompt Order will stick.