You don't need to (and definitely should not) copy and paste the code from that module into your own code. Are you familiar with BioPerl and using CPAN modules in your code in general? Otherwise the BioPerl HOWTOs would be a good place to start.
If you need to extend the capbilitiy of the module to fit your needs then you could subclass and extend it. If you describe your use-case a bit more I'm sure we can give you some more specific help.