First of all. Get this version of YY-CHR:http://acmlm.kafuka.org/uploader/get.php?id=4307
there are some other vital programs in there, that you can ignore.
On the palette issue. The default palette is always false. You need to play your game in ZSNES, and make some ZST savestates. Usually this is done, when you see a sprite (that you want to edit) on-screen.
Now open YYchr, load the decompressed gfx in it (usually a bin file) and then go to Palette/Emulator state load and select the ZST savestate. Now press the down-arrow button to change all the available palettes with this savestate (if your sprite was on-screen, than one of the palettes is completely accurate to your sprite).