You will notice a big change when selecting options if you type in "java -version" after doing so. Soif you run update-alternatives --config java and select option 3, you will be using the Sun implementation.
Also, with regards to auto vs manual mode, making a selection should take it out of auto mode per this page stating:
When using the --config option, alternatives will list all of the choices for the link group of which given name is the master link. You will then be prompted for which of the choices to use for the link group. Once you make a change, the link group will no longer be in auto mode. You will need to use the --auto option in order to return to the automatic state.
And I believe auto mode is set when you install the first/only JRE/JDK.