Should the evaporator coil be installed 6" above the furnace?
If it's an upflow you don't have a choice in the matter. The evaporator coil will sit butted up directly on top of the furnace cabinet and that is factory install, no spacing required. And I'm not certain what you mean by the coil sitting inside of the duct other than sometimes the case/cabinet of a box coil is removed and the actual supply air plenum is put over the entire thing, with ducts running from it. It still sits at the exact same heigth with or without the case, directly sitting on top of the furnace.
Not the best way, cased coil is factory, but it has been done and it will work.