What you want is to edit your buildout to create a second instance to run. You'll need to add a ZEO server too, plus the necessary changes to your setup to have the instances connect to that port.
You cannot just change the configuration file to start a second instance on a different port otherwise; to run multiple instances you need, at the very least, a ZEO server or a RelStorage ZODB setup to be able to share access to the object database.
See the Plone developer manual on how to set up multiple instances and a ZEO server for your setup.
And if your buildout takes 15 minutes to run, then it sounds like your buildout is perhaps doing too much network connection checking. Try running it with the -N switch to switch off the default 'newer package' checks.
As for the configuration file used by bin/plonectl, that would be parts/plonectl/etc/zope.conf. Generally speaking, a bin/partname instance script is paired with a parts/partname directory, and Zope instances look for a etc/zope.conf file there for configuration. Altering files by hand in parts/partname directories will be lost when re-running buildout, as it'll generate new copies.