I'm doing the symlinks thing using GNU stow.
Basically i have all the packages in their own dirs in /usr/local.
For example qt in /usr/local/qt/3.3.4.
With stow i then symlink the whole stuff up into /usr.
This is working pretty fine for me except when you have packages that have dirs of the same name (this happens quite often with local).
Those dirs i have to create in /usr and stow then symlinks the packages into them.
Quite a lot of work in the beginning but now the system is up and running its quite easy to do.
Its quite possible to install all the stuff in separate dirs but you'll always be needing to symlink it back into the FHS dirs because so many programs just
assume the stuff is in there.

I had tried this before without symlinking but putting all the dirs into PATH,LDFLAGS and so forth but that was doomed.
Many packages would put all the LDFLAGS into their .la file as a dependency and once i removed a package mentioned i couldn't build against said
packages anymore.

You should take a look at GoboLinux and their install script, maybe you can modify it to suit your needs.