You can use both but they will conflict. They're written to the same place so if you install something from apt and then install a later version from cpan, you could bodge things up.
I don't do much Perl but in Python I certainly have the dilemma you're talking about: apt-vs-PyPI. I personally opt for apt whenever I can. It means I should get updates without having to remember to maintain each individual Python package. Not only that but it means that all my systems should be running on the same version of those packages.
It doesn't always work out. Sometimes you don't have new enough things in the repos or something you need just isn't packaged up. Neither way is perfect but I believe apt to be more perfect. Just be aware of what you're doing and you should be okay.
Edit - Almost forgot, there is a better way to section things up so the system can have its own environment and whatever you're developing can live in its own environment (that you manage completely with CPAN), Like Python's