Palette issues editing portraits and sprites

Hi all,
Brand new to modding FF6/3, forgive noob question.
Veteran unix admin, non-noob to general CS concepts.

So what I'm trying to do as a learning exercise is to simply swap the graphics for Leo and Cyan.

I've used FFSE Final Fantasy 3 Sprite Editor V 2.11 to do the swap of the portraits since no other editor seems to have this ability, however doing so screws up the palette for all kinds of things.
I've used FF3usME 6.8.0 to edit the walking/battle sprites without any trouble, but doing the portraits seems to be the only useful feature FF3usME lacks.

Anyone have advice on the best way to safely edit character portraits?