This is the Dark Side of package managing schemes; when the packages get out of sync with what's available fresh from the sources of the Source, you have to figure out what's more important to you: using the latest and greatest (in which case you *can* run unstable Debian, which is closer to the bleeding edge) or having a system that "knows what's installed" at all times? I *tend to* do a mixture of both (is that the worst of both worlds?) For software I know and love, or that I need to customize, I nab a tarball and compile it. For software I don't know, or need to Just Work, I use the packaging system (dpkg, rpm). As long as I don't put too much on my plate and start installing packages that look for the packaged version of software I manually installed, my system doesn't get into inconsistent states. But this can happen once you leave the safety of your package management system; it really is up to you to figure out whether the risks are worth it.

A happy medium is often available when the software maintainer, or the distribution 'vendor' provides source packages -- SRPMS and source .debs; you can get the latest, compile it for your system, and have all the package management goodies. I use this wherever possible (just yesterday I installed AxKit with XML::Sablotron on RedHat, and compiled Sablotron from the source RPM.) I haven't used src debs, but it's probably just as simple. And you always *can* download a package manually if apt-get won't get it for you =)

With the perl modules themselves, CPAN.pm provides decent package management, so you can offset the problems of the mixed system.

update Let me insert a plug for FreeBSD's ports system (which IIRC is available for other BSDs). It works in a manner similar to SRPMs, the BSD team maintains the ports (which may include various patches, and uses a fairly consistent scheme for binary placement etc.), and they're usually pretty up-to-date.

Did that help? Well, I didn't say much, but I tried to say why I can't say much =)

Philosophy can be made out of anything. Or less -- Jerry A. Fodor