Basically, if it works in your emulator, it'll work on the real cart.
Keep in mind the CHR is just the tiles, while the PRG is how those tiles are laid out, as well as the color palette being used.
So if you found the tiles that make up Mario's head, you could alter those and then your Mario would be running around with a different head.
Most games have a separate CHR and PRG chip. Keep in mind some games (like an UNROM based game) use RAM for the CHR, meaning there is really just one programmed chip and the CHR tiles ar copied (or created) there from the PRG.
The hack called Super Mario Clouds did the opposite. They left the CHR data alone and just modified the PRG code to display those sprites differently.
Al