I always copy one of the "most appropriate" other modules file structures of CPAN modules that I have and start making changes to that. At least that way it has all of the specifics that I need in my modules (e.g. copyright notice).
I think it is all about discipline, whether you use h2xs or your own solution.
One tip I've picked up from an article Johan Vromans wrote long ago: I have a "src" directory that contains all the sources of all modules that I work on. For each CPAN uploadable distribution I have a seperate directory structure. The .pm files in there are actually symlinks to the appropriate files in the "src" directory. This allows you to work from the distribution or from your "src" directory, whichever is more convenient to you at the time.
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