When you run pybombs for the first time, it should ask you what prefix you want it to install into. For example, i think it defaults to /usr/local/. This then passes that prefix directory to the configurare parameter "--prefix" for autotools based projects or the cmake parameter "-DCMAKE_INSTALL_PREFIX" for cmake based projects, and the projects install into that prefix. Pybombs is simply running the "configure/make/make install" for the project you want to install and all it's dependencies. There's no magic about where it installs things.
Tim