* Keep your own Perl (the one you use for your own projects) separate from the system Perl (the one Debian uses internally for its own purposes).

* Do not replace /usr/bin/perl with your own Perl. Your own Perl should be in /opt or ~/opt.

* Install your Perl into its own tree (ex. /opt/perl-5.10.0). From wherever your Perl source is located, you'll configure with something like ./Configure -Dprefix=/opt/perl-5.10.0. After installation, create a symlink next to your Perl dir named "perl" (ex. cd /opt; ln -s perl-5.10.0 perl).

* You probably want to set your own user's PATH to find your Perl (ex. /opt/perl/bin/perl) before the system's Perl -- but don't do that for the root user.

* You might now start all your scripts with the shebang line: #!/usr/bin/env perl, which tells it to find whichever Perl is first in your PATH.

* Update and install modules for the system Perl using only apt-get (or the newer aptitude). Never use cpanp with the system Perl.

* Install modules for your own Perl using only cpanp. Apt, of course, knows nothing of your own Perl -- nor should it.