Well after doing a lot of reading, the 'proper' way to install SUN's JAVA on Ubuntu is to use make-jpkg to convert them to deb. This also ensures the environmental paths end up all correct with no intervention. This is why the make-jpkg package is available.
The only package I have to install manually like you explained is J2EE.
Ubuntu Breeze 5.10 - - Java JDK/JRE/J2EE
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