When upgrading minor versions like this, you generally have nothing to worry about with respects to modules and scripts that might be tailored to the older version. When modules are written that are specialized with one particular version of Perl, or a specific architecture, they will place themselves in a version- or architecture-specific directory in your Perl lib directory (e.g. /usr/lib/perl5). Thus, you can usually have several different versions of Perl running simultaneously on the same system, as each one will only pay attention to its own version-specific subset of Perl modules. Other Perl modules that aren't version-specific sit high in, say, 'site_perl', and can be used by any version or architecture of Perl. This also allows for a reasonable attempt at sharing the same Perl lib directory across the network for multiple systems on multiple architectures with multiple Perl versions, if you so desire.
So in other words, I wouldn't worry about removing old stuff before installing new stuff. In fact, most major production installations tend to keep both versions around (with Perl binaries referenced as, say, perl5.00503 and perl5.6.1), so that older code that might have a problem with the new version can easily just point itself back to the old Perl binary and still function fine. The only caveat is that a great number of your modules will have to be re-installed/re-built after your upgrade, to populate the 5.6.x library hierarchy, but you'd have to do that anyway with a fresh install.
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