Installing Sun's java 6 on Linux is as easy as invoking apt-get but only if you are using Ubuntu since Sun and Ubuntu agreed to have Sun's Java to be included in the Ubuntu repositories.
However, for other distributions, it is not as easy. You may need to do a little more work to be able to install Sun's Java packages. HowToForge.com has a tutorial on installing Sun's Java as well as Netbeans on Fedora 7.
Now, there is no reason for you not to use the official Java implementation along with the "official" Java IDE. :)