If you use a combo with CSet 2 set as an FFC, then neither the on-map FFCs in ZQuest will show as if none of the combo is set to use CSet 2.
For this, I set the combo to use CSet2 on the top half, and the regular CSet on the bottom. Note that on the map, it's the same on the top and bottom.
Edit: It seems that Zelda-w doesn't respect it either. That said, I'm cool with them ignoring it, but then the combo preview in the editor, and the combo select screen would have to ignore it as well, as trying to use combos with CSet2 set is like trying to shoot a tiny target in the dark.