Generally you just arrange your modules under a 'lib' hierarchy in your distribution directory, and place any executables into a 'bin' directory. Then, in your MakeMaker options, use the EXE_FILES key, like:

       'EXE_FILES'    => [ 'bin/foo', 'bin/bar' ],
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Take a look at the Template Toolkit distribution for an example of a distribution with both executables and library modules.