Which distribution? Is it RedHat, SuSE, Debian, Ubuntu, something else? Most distributions have a package manager that allows you to update using command line (e.g. RPM on RedHat, dpkg on Debian / Ubuntu), but if we don't know which distribution you're using we can't tell you which commands to use.
This might nullify my previous question but java 1.6 is actually installed elsewhere on the server, as I have tomcat version 5.5 is there any way that I can point the tomcat server to 1.6 java?
would this cause compatibility issues with the older 5.5 tomcat ?
Java is designed to permit multiple brands/flavors/versions to be installed and used concurrently on a single machine. In other words, it's the exact opposite of Internet (There Can Be Only One) Explorer.
Tomcat will employ the JAVA_HOME environment setting that is in currently effect for the shell that launches it. So moving from JDK 1.5 to JDK 1.6 would be as simple as setting JAVA_HOME=/usr/java/jdk1.6.x for that shell. If Tomcat is being managed by an init script, examine the script to see how JAVA_HOME is being set.
I don't think Java6 is a problem for Tomcat 5.5, although it would be for Tomcat 5.0. However, it's better to upgrade to at least Tomcat6 just for support reasons.
An IDE is no substitute for an Intelligent Developer.