Using "Emacs Configure" **and** modifying .emacs

[Ronald Fischer]

I'm using the Emacs Configure method
(Options/ConfigureEmacs/BrowseCustomizationGroups) to configure Emacs.
However, some configurations settings must be done by manually setting
the customizataion variables (at least according the FAQ) in the .emacs
file. 

Now, the interactive emacs configuration **also** modifies .emacs. What
do I have to do to keep my settings and thos Emacs is writing, apart? I
don't want Emacs to override my settings, and I don't want the Emacs
configuration tool to get confused, just because my .emacs file contains
things I  have put there.

Ronald