There have been a few threads regarding ISO mounting, playback and the inability to include these files in TheaterView's View Schemes. With the addition of the new assignable "Playback Method" by File Type all the ISO problems are solved.
1) Change how MC13 handles launching ISO's: Tools --> Options --> File Types. Scroll down to the "Data" Section, Select "Disk Image Files" and change the Playback Method to "External Program (default)
2) Tag your ISO Files: Now with your ISO's ensure that the "Media Type" Library Field is set to the View Scheme you want (mostly Video but could be Audio if you ISO your CD's) for each file. Assign Coverart as normal and away you go, all your ISO's now apear in the correct area of TheaterView and will Mount, Launch and Play just as you would expect.
Thanks to the JR Team!
Nathan
PS - this assumes you already have your ISO mounter setup and working correctly
EDIT - Updated the Wiki
http://wiki.jrmediacenter.com/index.php/DVD_Library_in_Media_Center#ISO_file_in_MC13