This document describes how to run multiple instances (search for "Multiple Tomcat Instances").
You will need to configure the Tomcat 7 connector (not the builtin Tomcat connector), make sure you enable it. Then click the "Create Launch Configuration" button on the Launch page of the server connector configuration. On the configuration dialog, catalina.base can be defined on the Arguments tab, in the VM Arguments panel (there will already be a default definition there, that you can change). The deployment base folder can be defined on the Server tab. The catalina.base folder, as described in the linked document (as CATALINA_BASE), will have configuration files for Tomcat, so you should be able to define the port number there. Every launch configuration can be used as a server, by ensuring the "Add as server" checkbox is ticked on the Server tab of the configuration dialog. Name each configuration as you wish (presumably to include the port number).
I haven't actually tried this but I can't see why it wouldn't work.