TomHa,
Go to Window > Preferences > MyEclipse > Servers > Integrated Sandbox > MyEclipse Tomcat 6. You can see the location of MyEclipse Tomcat specified against ‘Tomcat Base Directory’. The server.xml can be found at < Tomcat Base Directory >/conf/server.xml.
I am afraid it cannot be shown in the project panel and you have to manually go edit it as suggested above.
Let us know if you see any issues.