I'm just gonna jump the gun and assume SNES since I have the time to type all of this out.
- Load the game in ZSNES (unfortunately Snes9x states aren't supported, I'm not sure about other emulators)
- Get to a place where the graphics you want to edit are loaded, save a state.
- Open a copy of your ROM in YY-CHR. Go to Palette -> Load Emulator state file or hit F12. Open the state you just saved.
- Switch Graphic format near the bottom of the program to 2BPP GB, 3BPP SNES, or 4BPP SNES depending on what you want to edit (see below)
- Go to the appropriate offset for what you want to edit.
- Select the palette that matches the graphics you're editing from the bottom right panel
- You can try using the pattern option to make this easier. For example, use FC/NES x8 for field character sprites. It's possible to make custom pattern files, but I'm lazy and usually just open a second instance of YY-CHR to use as a clipboard.
Here are the offsets for most of the sprites:
- 0x048200 - Monsters (3BPP)
- 0x0638C0 - Magic effects (3BPP)
- 0x0D0200 - Battle characters (4BPP)
- 0x0D8200 - Field characters (3BPP)
- 0x0E0200 - World map objects (3BPP)
- 0x0E5B00 - Battle weapons & effects (3BPP)
These offsets are headered, so if you're using an unheadered ROM, subtract 0x200 from them. Unfortunately, one thing YY-CHR does lack is an option to quickly go to an offset, so just use the scrollbar, pgup/down keys, arrow keys, and + and - keys to get to them. The current offset is displayed in the title bar.