If I were you and wanted utilize what I had, I'd install the fuse between the batteries and the charge controller and install the disconnect between the controller and the panels. Your way, I can almost guarantee that someday that disconnect will get opened while the panels are hooked up. As Mr. Wizard said, this could be bad. My suggested way makes it somewhat failsafe. You could even place a placard by the fuse warning not to remove it unless the panel disconnect is opened.
There is no problem having multiple charging sources on at the same time.
