Hello, hyakulegger. Welcome to Romhacking.net and the super special awesome world of SMB3 hacking.
There actually is an available SMB3 Music Editor program that was written by JaSp many years ago. He shared the last version that he made of it publicly back in 2009 through Board 2. You can download the utility at the following link:http://klikechange.free.fr/romhack/smb3asm/smb3me.exe
He shared it in the following topic, "Going after the SMB3 Music Format...":http://acmlm.kafuka.org/board/thread.php?id=5078
If you try searching through Google before you ask potential questions, you might discover other helpful little bits of relevant information here and there. When it comes to NES SMB3, many frequently asked questions have been answered and covered in the past, and as henke37 likes to point out in most recent SMB3 related threads, there is a disassembly for the game out there that you can also locate.
JaSp also created the SMB3 Music Inserter, but that program is designed specifically for the expanded Reuben SMB3 ROM. Since your current intention is to only modify the graphics and music, unless you want to make use of expanded CHR-ROM space to further customize your graphical modifications, you most likely don't need to use an expanded Reuben SMB3 ROM. Nonetheless, the thread for the utility, also last active in 2009, can be viewed here:http://acmlm.kafuka.org/board/thread.php?id=5813
Best of luck! You can do it!