In case anybody is looking for a way to run pylint as an external tool in PyCharm and have it work with their virtual environments (why I came to this question), here's how I solved it:
$PyInterpreterDirectory$/pylint
--rcfile=$ProjectFileDir$/pylintrc -r n $FileDir$
$FileDir$
Now using pylint as an external tool will run pylint on whatever directory you have selected using a common config file and use whatever interpreter is configured for your project (which presumably is your virtualenv interpreter).