There’s a better workaround so you can keep Ubuntu’s Tomcat6 (taken from http://ubuntuforums.org/showthread.php?p=8541057, by DisDis)
In a terminal:
sudo apt-get install tomcat6
cd /usr/share/tomcat6
sudo ln -s /var/lib/tomcat6/conf conf
sudo ln -s /etc/tomcat6/policy.d/03catalina.policy conf/catalina.policy
sudo ln -s /var/log/tomcat6 log
sudo chmod -R 777 /usr/share/tomcat6/conf
There. Now just go to Window/Preferences/Sever/Runtime Environments, add the Apache Tomcat6 Server and use /usr/share/tomcat6 as the installation directory!