You don't want the repository install of Tomcat if you plan on using Netbeans to control it. Netbeans expects it all to be under one directory.
I usually download the latest version of Tomcat from the Apache website and put it under $HOME/Software (the location doesn't really matter).
Edit the tomcat-users.xml in the Tomcat conf directory to be something like this:
It's only the role that has to be "manager", the username and password can be anything.
<user username="admin" password="manager" roles="manager"/>
Then add Tomcat as a server to Netbeans, for example specifying "$HOME/Software/apache-tomcat-6.0.26" as Catalina Home and "admin" as the admin username, "manager" as the password. You might also need to modify the port numbers if you have other things listening on Tomcat's default of 8080.