This is an issue that was recently discussed in yast vs cpan in which I offered this comment. I actually use Debian, too (unstable x86-64, aka etch), but the comments in that node are relevant to any distro. I'll reiterate only a little bit here: Have a completely separate development space. Let Debian do its own thing with regards to modules and you keep your own compiled perl and CPAN'd modules somewhere saparate (your ~/ maybe?).
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