Yes, you can run multiple instances of tomcat in eclipse:
Go to window->preferences. Set the tomcat home & config file for the 1st instance.
Start tomcat. Once it's started
Go to window->preferences. Set the tomcat home & config file for the 2nd instance (which should be a different directory)
Start tomcat again. Now you should have 2 versions of tomcat running.
It's that simple--but I'm not sure if debugging will work, you'll have to try it out by putting breakpoints