While I never did graphics or palette hacks, I do have some experience doing Sega Genesis asm hacks.
I use the MESS / MAME debugger for it.
First you will need to find some RAM addresses related to the colors you want to hack.
Then you use these addresses in the debugger. Some 68k asm understanding is needed.
When you find the related instruction or values that need to be changed, its the time to open the ROM with your favourite hex editor to modify it.
Sorry if I cannot help you further, as I said I never did graphics hacks.
I wish you good luck with this project.