Avoid the whole mess and keep two perl installs. Have the system perl (/usr/bin/perl or /usr/local/bin/perl) which aptitude maintains. Then, have your own personal perl (~/bin/perl) which has your own modules. Check out Perl::Install for an easy way to install it. Patches welcome.
My criteria for good software:
Does it work?
Can someone else come in, make a change, and be reasonably certain no bugs were introduced?