I found the following for installing a sample program:

alternatives --install /etc/alternatives/editor myeditor /usr/bin/kwrite 90

So for the above it would be something like:

alternatives --install /etc/alternatives/java java  usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/bin/java 10

alternatives --install /etc/alternatives/javaws javaws  usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0/jre/bin/javaws 10

Then use the alternatives command to specify the new packages as the default.

 (I really wish the packagers would automatically tell alternatives about the new java, most of the major distributions currently use it (alternatives))