Homebrew and existent software in /usr/local
It would probably work ok to mix the two, but to be safe I'd just put homebrew in a different directory.  You might run into conflicting files, perhaps in some supporting library.

I don't know what's special about your mysql build, but i'm sure homebrew has options to build different flavors.  do "brew options mysql" to see what is available, perhaps it has what you need.