[Doc Holliday]

Not exactly sure of what you mean. Is this a vertical upflow system? Any pics you can provide?

 

[Doc Holliday]

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.

 

[Doc Holliday]

Btw, people tend to remove the casing of the coil when they don't have the correct size dimensions to match up to the furnace. Three sides, the left, right and the back casing of an upflow evaporator coil should be FLUSH to the same three sides of the furnace. The front side will sit back on top of the furnace, behind the flue pipe.

Your furnace has a lip on the top so the evaporator fits perfectly onto it.