According to its manpage, perldoc will search in any directories in the environment variable PERL5LIB. So if you wanted some POD documentation in a Pod directory or a doc directory and some mixed into libraries in lib and other mixed into executables in bin, you could just write a small script that did: 
    PERL5LIB=./Pod:./lib:./bin perldoc "$@"

[download]
to tell perldoc to search in those three places.

In reply to Re: Layout of "pure pod" files in a hierarchy? by sgifford
in thread Layout of "pure pod" files in a hierarchy? by deprecated

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