From the homebrew FAQ (https://github.com/mxcl/homebrew/wiki/FAQ)

    Can I install my own stuff to /usr/local?

    Yes, brew is designed to not get in your way so you can
    use it how you like.

    Install your own stuff, but be aware that if you
    install common libraries, like libexpat yourself, it may
    cause trouble when trying to build certain Homebrew
    formula. As a result brew doctor will warn you about
    this.

    Thus it’s probably better to install your own stuff to
    the Cellar and then brew link it. Like so:

        $ cd foo-0.1
        $ brew diy
        ./configure --prefix=/usr/local/Cellar/foo/0.1
        $ ./configure --prefix=/usr/local/Cellar/foo/0.1
        [snip]
        $ make && make install
        $ brew link foo
        Linking /usr/local/Cellar/foo/0.1... 17 symlinks created

And really, writing your own formula is easy if manual steps are easy, and if they're hard, well, writing a formula makes you do it only once, since you'll be able to reuse the formula later.

Anyway brew builds in Cellar, and symlinks in /usr/local but never steps on what you would have installed manually.