@cirkit:
As I went through the thread I understand it is easier and faster to reinstall and restore config.xml to the second harddrive but does this method automatically install all packages and rules associated to them. Say for eg I have squid + dandguardian + sarg + nut + cron.
As I understand it yes, it does. I tried it twice, but it didn't work out for me; it kept on installing and deinstalling and installing. Which made me conclude it is sort of 'macro-wise' replaying all config changes done (or something like that, I am still a noob ;D).
I ended up doing fresh installs. What I could recommend is backup all sections of the config individually (see GUI); that did come in handy for me for restoring the static IP's in my LAN's. For the remainder, I just manually reinstalled everything.