I really don’t know because I never needed/wanted to run both engines in parallel. Maybe somebody can chime in that has experience with that.
But if I would need it, what I would do for sure is: run It with CommandBox. As far as I know CommandBox is the perfect software for this. It uses one servlet engine for both worlds, abstracting all settings by using a simple json configuration file. If you want to switch the cfengine, you just change the cfengine attribute in the json file. Also, it isolates each webroot into one and only servlet engine instance. Then it creates just one web context per imstance, so that no webroot would/could mess around with the other.