You can write the module either before or after you use h2xs. I've done both. When the docs are so strident about using h2xs, they're primarily referring to using it for modules that you are going to distribute (see "How To Write a Makefile.PL" in perldoc ExtUtils::MakeMaker).
If you've already written your module, then use h2xs, though to be frank, using this utility before you start to write the module is easier because the Test::Harness is all ready to go, thus writing tests and using make test is sooooo much simpler.
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