There will only be one Tomcat 5.x listed in the “servers” view at one time, but you can launch 2 separate Tomcat 5.x instances using the launch configurations. Here is how you can do that.
1) Open up the Tomcat 5 Connector preference page
2) Configure the tomcat connector to point to the 1st instance of tomcat
3) Set it to Enable and press Apply
4) Then expand the Tomcat 5 pref page node and select Launch
5) Select the “Create Launch Configuration” button
6) When the launch config dialog opens, Change the name from Tomcat 5 to “Tomcat 5 Instance 1” or whatever, select “Apply” and close the dialog
7) Go back to the main tomcat connector page and change the Tomcat home directory to the 2nd instance
8) repeat steps 2-6 for the 2nd instance, be sure and name the 2nd launch config “Tomcat 5 Instance 2”
Now go to Run > Debug…, and under the MyEclipse Server node, you should see your 2 tomcat instances. You can click on either one and launch that instance of tomcat. Hope this helps.