Do the developement in a perl module and write a pl file to execute the code after testing. That means 3 files; .t, .pm, and .pl where the Ruby guys only needed 2.

The 3+ file option is best in Perl IMHO. Who cares if you have three files or only two? Actually, it is often best to have more than three files. That is, to write a number of .t files for each .pm file. Why? Because maintaining a number of (small) .t files, one to test each aspect of a module, is usually easier to manage and maintain than a single (monolithic) .t file. I favour this general approach in any language, including Ruby.

When writing Perl scripts, I typically abstract the work they do into CPAN-like modules and unit test each module using Test::More and the prove command. I strive to keep my script mainlines as short as is practicable. There are many examples of this approach on the CPAN; see, for example, the perltidy command, part of the Perl::Tidy distribution and the perlcritic command, part of the Perl::Critic distribution.

At work I would like to create my own modules but I was told to have everything in one file for the application I've been working on.

Why? That looks like very poor advice to me.