There are 2 types of files associated with QueryPlus:              

Query files (.qpe)              

Report Designer files (.mrt)

Query files are stored in the QueryPlus SQL Server database and will be backed up when and if the database is.
Query files can be manually backed up within QueryPlus by selecting Reports – Backup Reports and selecting a location at the prompt.
All of the Query files will be exported to that locationReport files are stored at a location determined by the QueryPlus user, usually a network or local hard drive.

My recommendation for a backup plan would be 3-fold:                                                              

1. Set up a regularly scheduled backup of the QueryPlus SQL Server database.                                                            
2. Store the Report Designer files on a network drive that is automatically backed up.                                                           
3.  Periodically perform a manual backup of the Query files from within QueryPlus.