Debian Installation :: Replace Only The Change Files From The Archive?

If I understand everything right I can use simple cd to create an install of my system then config everything and create an archive of /etc,/var,/usr and that give me a backup of my changed files. but what I am not able to do is create a script to replace the files with the archived version of the config files automatically. I need it to be ran as a post intall script or to configure the conf files as part of the install. what I configure on every reinstall. apache,proftpd,mysql,php,and wordpress. Since I am still learning I reinstall a lot and standard backups have not been working for me. But I can put the whole install including backup on one cd. Is there a way replace only the change files from the archive. or getting a list of just the modafied files on my system.