You may need to be more specific about your goals, but from what you've said, I do not think you can have a single script execute partly in one CMD window and partly in another one in the way you mention. If you want multiple versions of a script operating you should look into
fork[
^]which will let you create a new child process running the same script from the same point as the original parent. Note that this requires some care in what you are doing to keep the various copies coordinated and controlled!
However you could have one script create a shell that then executes another script, something like this trivial example:
perl -e "system 'start CMD /k perl -v'"
If you run that as a command at your CMD prompt, it will open a new independent CMD window and cause it to run Perl with the -v option, and then remain open afterwards (or use /c to close after the run - check HELP CMD for other options). You could replace the -v with the name of another Perl script to execute.