It would help to know where the enemies are stationed on that map.
Anyway, here's what you have to do:
1) Setup a control sector (just like you'd do when making an FOF), give one of its linedefs the
"Intangible Invisible" FOF action. The tag of this FOF should be linked to a target sector/area where the boss is or roams about.
Note: The intangible FOF is used to scan for any enemies (including bosses) inside it.
Now on another linedef in this control sector, give it the
"No More Enemies - Once" trigger action. A tag is not needed on this linedef.
2) Create another control sector, give one it the
"Trigger Linedef Executor - Once" action. The tag number given to this linedef should be the length of the "No More Enemies - Once" trigger linedef.
E.g. If the no more enemies linedef is 5 fracunits long then the tag on the trigger linedef executor once should be 5.
On another linedef in this control sector, give it the
"Shatter FOF" action. This linedef doesn't use tags the normal way.
In fact you have to use the texture offsets to tag the control sector and target sector of the FOF you want to shatter separately. The x-texture offset is used to determine the tag of the target sector and the y-texture offset is used to determine the control sector.
If you set this up correctly then when you defeat the boss the FOF that you want to shatter, should be seen crumbling apart like bustable/shatter block.
Here's an example wad that I quickly created:
http://www.mediafire.com/file/bsxubx99qq93mkn/BTE.wad
When you defeat the enemies in the area you spawn in, the FOF should break apart.