Don't most packages have a configuration option in their config script that tells it what directory to install to? Like, when I was compiling GIMP (don't get excited at the sound of that - it runs but clicking into it breaks touch input inside other programs and itself, so that's at a standstill until I get around to working on it more) for the N900 you could tell it what filepath prefix to use with a config parameter before compiling. For every package that does, you can just manually add that flag when running config, and then make and make install from there.