Two points from Perl Best Practices (Documentation section) you might want to contemplate:

• Distinguish user documentation from technical documentation.
• Place POD as close as possible to the end of the file.

Personally, I dislike intermingling POD with code. Documentation of code is for programmers, so I use simple Perl comments (not POD) for that, right by the code it is documenting. Makes it easier to update the comments in step with the code.

Technical documentation of the system architecture (not the code) I place in a single large POD documentation section at the end of the file, or in a separate file.

User documentation should be kept separate from technical documentation. For that, I suggest either a separate POD file (or a big POD block at the end of the source file) ... or simply a Usage subroutine displayed when the user enters --help at the command line, making the user documentation more discoverable and more likely to be read.

See also:

• Ten Essential Development Practices by Damian Conway
• Re: looking for feedback on my first script