davout,
1. You cannot create a Launch Configuration for the MyEclipse Tomcat Server. Because it’s an internal server and all trimmed down, we block you from being able to create it so it won’t show up in the Run/Debug dialogs.
2. If all you want to do is setup environment variables for your app server, you can do that from the standard connector dialog under the JDK arguments page by adding -D command line arguments, they will be loaded by the VM as env variables (e.g. -Duser.name=jeffb)
3. If you really want to use a Launch Config, you should probably grab Tomcat 6 or Tomcat 6+ from the Apache site and setup the Tomcat connector and do the launch config from there.
Let us know how it works for you.