well just use the various adb commands in Terminal :) Just type in "adb", press enter and you'll get a list of all possible commands. Assuming you've added the path to your sdk tools folder to your bash profile. Otherwise just drag & drop the adb binary from the tools folder onto your Terminal window, et voila.
The most used commands are probably push and pull where you can, well, push stuff to your phone or pull it to your computer.
So if you want to modify the boot.mp3 you would pull the original from the phone to your computer, modify it and push it back, overwriting the original file. In Terminal speak: ;)
adb pull /system/media/bootscreen/boot.mp3
adb push /path/to/boot.mp3 /system/media/bootscreen/boot.mp3
Please note depending on the ROM you're using the paths may be different. To browse the device via Terminal type in "adb shell" and make a simple "ls" to list the directories, "cd" to change directories etc.
Or if you just want to use another mp3:
adb push /path/to/whatever.mp3 /system/media/bootscreen/boot.mp3
Again, on the Mac you can just drag & drop files onto the Terminal to get their full Unix paths like to your custom mp3