apt-get, aptitude, etc. will install the modules to the system libraries. If you are installing from your distribution's repositories, this should be fine - they should not conflict with your system requirements. I don't know that you can, easily, have them install to alternate locations. You could customize the packages and install from a personal repository, but that's not trivial.

You can configure cpan to install to your home directory. Look for I am not root, how can I install a module in a personal directory? in CPAN.

Others report success with local::lib. I haven't tried it, but it looks made for the purpose.