Thanks for the help, Xifanie's program definitely helped a lot on changing the battle palette. As to changing the formation palette, I don't know what method you were going to suggest, but I didn't find this to be much work or difficulty at all, so I'll go ahead and post what I did just in case:
Use FFTEVGRP to open UNIT.BIN and go to the sprite you want to change the palette of. Save the palette (PAL file). Open it in a hex editor and starting at location 0x16 you're looking at the RGB values for each of the 16 colors in sequence (separated by a byte '00'). Now just take whatever value you used in Xifanie's program for that color and multiply by 8, then convert to hex. Pop em all in, re-import the palette in FFTEVGRP, and voila. Your formation sprite now has the same palette as the battle sprite.
Use FFTEVGRP to open UNIT.BIN and go to the sprite you want to change the palette of. Save the palette (PAL file). Open it in a hex editor and starting at location 0x16 you're looking at the RGB values for each of the 16 colors in sequence (separated by a byte '00'). Now just take whatever value you used in Xifanie's program for that color and multiply by 8, then convert to hex. Pop em all in, re-import the palette in FFTEVGRP, and voila. Your formation sprite now has the same palette as the battle sprite.