One thing that may not be clear to you is that a JRE is a proper subset of a JDK.
This means that all of the functionality (and files) that exist in a JRE also exist in
a JDK. The JDK has the additional files necessary to compile your Java Applications.
If you want to install a 1.6 JRE, or JDK you can do so, just not to the same directory that exists and contains your 1.5 JDK or JRE.
Install it to a separate directory, and you should be just fine.
Right now, I have a 1.4.2 JDK directory, and a 1.5 JDK directory, and a 1.6 JDK
directory all installed (and usable) on my machine. To use one, I just set up
my environment variables to point to the appropriate directory structure.
Hopefully this helps.