If I understand your problem, I think this is the relevant documentation you want: CGI /MIXING_POST_AND_URL_PARAMETERS.

Better to stay away from Vars in CGI.pm: When using this, the thing you must watch out for are multivalued CGI parameters. Because a hash cannot distinguish between scalar and list context, multivalued parameters will be returned as a packed string, separated by the "\0" (null) character. Use the regular param function/method or Dump if you're just exploring, debugging.